Package: adductData
Version: 1.24.0
Depends: R (>= 3.6)
Imports: ExperimentHub (>= 1.9.0), AnnotationHub (>= 2.13.10), stats
(>= 3.5.0), utils (>= 3.5.0), methods (>= 3.5.0), datasets (>=
3.5.0)
Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5)
License: Artistic-2.0
MD5sum: b5b1a57cf1f85c116d139bd0e8ae5a57
NeedsCompilation: no
Title: Data from untargeted MS of modifications to Cys34 of serum
albumin
Description: mzXML files from Grigoryan et al 2016 (Anal Chem).
biocViews: ExperimentData,MassSpectrometryData,ExperimentHub
Author: Josie Hayes
Maintainer: Josie Hayes <jlhayes1982@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/adductData
git_branch: RELEASE_3_21
git_last_commit: 525af61
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/adductData_1.24.0.tar.gz
vignettes: vignettes/adductData/inst/doc/adductData.html
vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/adductData/inst/doc/adductData.R
dependsOnMe: adductomicsR
dependencyCount: 66
Package: affycompData
Version: 1.46.0
Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
License: GPL (>= 2)
MD5sum: 947b97ebad8131d287e9c1e82927c30f
NeedsCompilation: no
Title: affycomp data
Description: Data needed by the affycomp package.
biocViews: MicroarrayData
Author: Rafael A. Irizarry <rafa@ds.dfci.harvard.edu> and Zhijin Wu
<zwu@stat.brown.edu> with contributions from Simon Cawley
<simon_cawley@affymetrix.com>
Maintainer: Robert D Shear <rshear@ds.dfci.harvard.edu>
URL: https://bioconductor.org/packages/affycompData
BugReports: https://github.com/rafalab/affyCompData/issues
git_url: https://git.bioconductor.org/packages/affycompData
git_branch: RELEASE_3_21
git_last_commit: ec03144
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/affycompData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: affycomp
dependencyCount: 8
Package: affydata
Version: 1.56.0
Depends: R (>= 2.4.0), affy (>= 1.23.4)
Imports: methods
Suggests: hgu95av2cdf, hgu133acdf
License: GPL (>= 2)
MD5sum: 25ca5f5b63ed7be230c52690948ab1c2
NeedsCompilation: no
Title: Affymetrix Data for Demonstration Purpose
Description: Example datasets of a slightly large size. They represent
'real world examples', unlike the artificial examples included
in the package affy.
biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData
Author: Laurent Gautier <laurent@cbs.dtu.dk>
Maintainer: Robert D Shear <rshear@ds.dfci.harvard.edu>
URL: https://bioconductor.org/packages/affydata
BugReports: https://github.com/rafalab/affydata/issues
git_url: https://git.bioconductor.org/packages/affydata
git_branch: RELEASE_3_21
git_last_commit: f72e431
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/affydata_1.56.0.tar.gz
vignettes: vignettes/affydata/inst/doc/affydata.pdf
vignetteTitles: affydata primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affydata/inst/doc/affydata.R
dependsOnMe: affyContam
suggestsMe: affy, affycoretools, affyPLM, arrayMvout, Biostrings,
gcrma, Harman, mimager, puma, pvac, TurboNorm, vsn, RobLoxBioC
dependencyCount: 12
Package: Affyhgu133A2Expr
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: dc7b712a632c5abb300beedd87bbccfb
NeedsCompilation: no
Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data
Package
Description: Contains pre-built human (GPL571) databases of gene
expression profiles. The gene expression data was downloaded
from NCBI GEO and preprocessed and normalized consistently. The
biological context of each sample was recorded and manually
verified based on the sample description in GEO.
biocViews: Genome, Homo_sapiens_Data, GEO
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr
git_branch: RELEASE_3_21
git_last_commit: 7ffe34e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Affyhgu133A2Expr_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: Affyhgu133aExpr
Version: 1.46.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: 6b735e8aaf93c9911afe3f7af5eb0743
NeedsCompilation: no
Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package
Description: Contains pre-built human (GPL96) database of gene
expression profiles. The gene expression data was downloaded
from NCBI GEO, preprocessed and normalized consistently. The
biological context of each sample was recorded and manually
verified based on the sample description in GEO.
biocViews: Homo_sapiens_Data, GEO
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr
git_branch: RELEASE_3_21
git_last_commit: 50eda27
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Affyhgu133aExpr_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: Affyhgu133Plus2Expr
Version: 1.42.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: 37d89dcfc3e2737a2bdb35535f9dcb98
NeedsCompilation: no
Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package
Description: Contains pre-built human (GPL570) database of gene
expression profiles. The gene expression data was downloaded
from NCBI GEO and preprocessed and normalized consistently. The
biological context of each sample was recorded and manually
verified based on the sample description in GEO.
biocViews: Genome, Homo_sapiens_Data, GEO
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr
git_branch: RELEASE_3_21
git_last_commit: a125395
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Affyhgu133Plus2Expr_1.42.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: AffymetrixDataTestFiles
Version: 0.46.0
Depends: R (>= 2.5.0)
License: LGPL-2.1
MD5sum: f9c26b20f4a890a3e918ff04252343b5
NeedsCompilation: no
Title: Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing
Description: This package contains annotation data files and sample
data files of Affymetrix file formats. The files originate
from the Affymetrix' Fusion SDK distribution and other official
sources.
biocViews: ExperimentData, MicroarrayData
Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel
Hansen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles
git_branch: RELEASE_3_21
git_last_commit: dbafce5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/AffymetrixDataTestFiles_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: affxparser, affyILM, aroma.affymetrix
dependencyCount: 0
Package: Affymoe4302Expr
Version: 1.46.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: f6a9be82e70995c7fd0ae847f419307e
NeedsCompilation: no
Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data
Package
Description: Contains pre-built mouse (GPL1261) database of gene
expression profiles. The gene expression data was downloaded
from NCBI GEO, preprocessed and normalized consistently. The
biological context of each sample was recorded and manually
verified based on the sample description in GEO.
biocViews: Genome, Mus_musculus_Data, GEO
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affymoe4302Expr
git_branch: RELEASE_3_21
git_last_commit: dc720b5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Affymoe4302Expr_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: airway
Version: 1.28.0
Depends: R (>= 3.5.0), SummarizedExperiment
Suggests: knitr, GEOquery, markdown
License: LGPL
MD5sum: f088919ee1fa9013bb2295f267c0d565
NeedsCompilation: no
Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle
cells, by Himes et al PLoS One 2014
Description: This package provides a RangedSummarizedExperiment object
of read counts in genes for an RNA-Seq experiment on four human
airway smooth muscle cell lines treated with dexamethasone.
Details on the gene model and read counting procedure are
provided in the package vignette. The citation for the
experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q,
Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C,
Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST,
Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a
Glucocorticoid Responsive Gene that Modulates Cytokine Function
in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun
13;9(6):e99625. PMID: 24926665. GEO: GSE52778.
biocViews: ExperimentData, SequencingData, RNASeqData, GEO
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/airway
git_branch: RELEASE_3_21
git_last_commit: 4896ff2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/airway_1.28.0.tar.gz
vignettes: vignettes/airway/inst/doc/airway.html
vignetteTitles: Airway smooth muscle cells
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/airway/inst/doc/airway.R
dependsOnMe: rnaseqGene
importsMe: consensusDE, NetActivity
suggestsMe: apeglm, awst, biobroom, BioCor, BiocSet, CeTF,
DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser,
ExperimentSubset, funOmics, geyser, gg4way, ideal, IHW,
InteractiveComplexHeatmap, iSEEde, iSEEpathways, iSEEu,
OPWeight, pathwayPCA, pcaExplorer, PCAtools, plyxp, progeny,
ReducedExperiment, runibic, Rvisdiff, SummarizedExperiment,
TTMap, weitrix, XAItest, IHWpaper, RegParallel, seqgendiff
dependencyCount: 36
Package: ALL
Version: 1.50.0
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Suggests: rpart
License: Artistic-2.0
MD5sum: 5c2b983e5ffda7fd346beaaa937f1f4d
NeedsCompilation: no
Title: A data package
Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the
Ritz Laboratory at the DFCI (includes Apr 2004 versions)
biocViews: ExperimentData, CancerData, LeukemiaCancerData
Author: Xiaochun Li
Maintainer: Robert Gentleman <rgentlem@gmail.com>
git_url: https://git.bioconductor.org/packages/ALL
git_branch: RELEASE_3_21
git_last_commit: 81e0f2f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ALL_1.50.0.tar.gz
vignettes: vignettes/ALL/inst/doc/ALLintro.pdf
vignetteTitles: ALL data intro
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ALL/inst/doc/ALLintro.R
importsMe: ConsensusClusterPlus, dGAselID, scRNAtools
suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet,
Category, CellMapper, ChromHeatMap, clipper, EnrichmentBrowser,
esetVis, genefilter, GeneSelectMMD, GOstats, graphite, GSAR,
GSEAlm, MLInterfaces, npGSEA, pathRender, ReportingTools,
rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv
dependencyCount: 7
Package: ALLMLL
Version: 1.48.0
Depends: R (>= 2.10), affy (>= 1.23.4)
License: GPL-2
MD5sum: b8d6c3f9a3cba2faa90ed88279c7cc19
NeedsCompilation: no
Title: A subset of arrays from a large acute lymphoblastic leukemia
(ALL) study
Description: This package provides probe-level data for 20 HGU133A and
20 HGU133B arrays which are a subset of arrays from a large ALL
study. The data is for the MLL arrays. This data was published
in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A.
Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami
Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James
R. Downing (2003) Classification of pediatric acute
lymphoblastic leukemia by gene expression profiling Blood 102:
2951-2959
biocViews: ExperimentData, CancerData, LeukemiaCancerData,
MicroarrayData
Author: B. M. Bolstad <bolstad@stat.berkeley.edu
Maintainer: B. M. Bolstad <bmb@bmbolstad.com>
git_url: https://git.bioconductor.org/packages/ALLMLL
git_branch: RELEASE_3_21
git_last_commit: f145b66
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ALLMLL_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQualityMetrics, pvac
dependencyCount: 12
Package: AmpAffyExample
Version: 1.48.0
Depends: R (>= 2.4.0), affy (>= 1.23.4)
Suggests: hgu133acdf
License: LGPL (>= 2)
MD5sum: 8c4fcc9e102a4a23b1f434fea297f277
NeedsCompilation: no
Title: Example of Amplified Data
Description: Six arrays. Three from amplified RNA, three from the
typical procedure.
biocViews: ExperimentData, MicroarrayData
Author: Rafael A. Irizarry <rafa@ds.dfci.harvard.edu>
Maintainer: Robert D Shear <rshear@ds.dfci.harvard.edu>
URL: https://bioconductor.org/packages/AmpAffyExample
BugReports: https://github.com/rafalab/AmpAffyExample/issues
git_url: https://git.bioconductor.org/packages/AmpAffyExample
git_branch: RELEASE_3_21
git_last_commit: f8a3c2d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/AmpAffyExample_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: AffyRNADegradation
dependencyCount: 12
Package: AneuFinderData
Version: 1.36.0
Depends: R (>= 3.3)
License: file LICENSE
MD5sum: 0a7e49261b41216a7c18f3ac974275f9
NeedsCompilation: no
Title: WGSCS Data for Demonstration Purposes
Description: Whole-genome single cell sequencing data for demonstration
purposes in the AneuFinder package.
biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data,
SequencingData
Author: Aaron Taudt
Maintainer: Aaron Taudt <aaron.taudt@gmail.com>
git_url: https://git.bioconductor.org/packages/AneuFinderData
git_branch: RELEASE_3_21
git_last_commit: a2b8d1b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/AneuFinderData_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: AneuFinder
dependencyCount: 0
Package: antiProfilesData
Version: 1.44.0
Depends: Biobase,
Suggests: frma, GEOquery, GEOmetadb
License: Artistic-2.0
MD5sum: 6933c239d2cfa4cbfa0cfdff0ec40191
NeedsCompilation: no
Title: Normal colon and cancer preprocessed affy data for antiProfile
building.
Description: Colon normal tissue and cancer samples used in Corrada
Bravo, et al. gene expression anti-profiles paper: BMC
Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.
Measurements are z-scores obtained from the GeneExpression
Barcode in the 'frma' package
biocViews: ExperimentData, MicroarrayData, Tissue, CancerData,
ColonCancerData
Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry
Maintainer: Hector Corrada Bravo <hcorrada@gmail.com>
git_url: https://git.bioconductor.org/packages/antiProfilesData
git_branch: RELEASE_3_21
git_last_commit: 56cc434
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/antiProfilesData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: antiProfiles, epivizr, epivizrChart, messina
dependencyCount: 7
Package: aracne.networks
Version: 1.34.0
Depends: R (>= 3.3), viper
License: file LICENSE
MD5sum: 2a1e49c2b55599139eafcc1889fdfddf
NeedsCompilation: no
Title: ARACNe-inferred gene networks from TCGA tumor datasets
Description: This package contains ARACNe-inferred networks from TCGA
tumor datasets. It also contains a function to export them into
plain-text format.
biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData
Author: Federico M. Giorgi
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>, Mariano
Alvarez <reef103@gmail.com>
git_url: https://git.bioconductor.org/packages/aracne.networks
git_branch: RELEASE_3_21
git_last_commit: 8adad99
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/aracne.networks_1.34.0.tar.gz
vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf
vignetteTitles: Using aracne.networks
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R
dependencyCount: 87
Package: ARRmData
Version: 1.44.0
Depends: R (>= 3.0.0)
License: Artistic-2.0
MD5sum: 6cfa96b213b0183de82248da05427075
NeedsCompilation: no
Title: Example dataset for normalization of Illumina 450k Methylation
data
Description: Raw Beta values from 36 samples across 3 groups from
Illumina 450k methylation arrays
biocViews: ExperimentData, MethylationArrayData
Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe
Maintainer: Jean-Philippe Fortin <jfortin@jhsph.edu>
git_url: https://git.bioconductor.org/packages/ARRmData
git_branch: RELEASE_3_21
git_last_commit: 6c8d3a4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ARRmData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ARRmNormalization
dependencyCount: 0
Package: AshkenazimSonChr21
Version: 1.38.0
Suggests: knitr, VariantAnnotation
License: Artistic-2.0
MD5sum: da5c19708c6c3495be1b1ce07dd3ad72
NeedsCompilation: no
Title: Annotated variants on the chromosome 21, human genome 19,
Ashkenazim Trio son sample
Description: SonVariantsChr21 is a dataset of annotated genomic
variants coming from Complete Genomics whole genome sequencing.
Data comes from GIAB project, Ashkenazim Trio, sample HG002 run
1. Both vcf and annotated data frame are provided.
biocViews: GenomicVariation, Sequencing, WholeGenome
Author: Tomasz Stokowy
Maintainer: Who to complain to <tomasz.stokowy@k2.uib.no>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21
git_branch: RELEASE_3_21
git_last_commit: 8d96b53
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/AshkenazimSonChr21_1.38.0.tar.gz
vignettes: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.pdf
vignetteTitles: RareVariantVis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.R
dependencyCount: 0
Package: ASICSdata
Version: 1.28.0
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown, BiocStyle
License: GPL (>= 2)
MD5sum: c97b6cdd24bb4647efd3bd079ffa9d09
NeedsCompilation: no
Title: Example of 1D NMR spectra data for ASICS package
Description: 1D NMR example spectra and additional data for use with
the ASICS package. Raw 1D Bruker spectral data files were found
in the MetaboLights database
(https://www.ebi.ac.uk/metabolights/, study MTBLS1).
biocViews: ExperimentData, Homo_sapiens_Data
Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie
Villa-Vialaneix [aut]
Maintainer: Gaëlle Lefort <gaelle.lefort@inra.fr>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ASICSdata
git_branch: RELEASE_3_21
git_last_commit: 71150d9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ASICSdata_1.28.0.tar.gz
vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html
vignetteTitles: ASICSdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ASICS
dependencyCount: 0
Package: AssessORFData
Version: 1.26.0
Depends: R (>= 3.5.0), RSQLite (>= 1.1)
Imports: DECIPHER, utils
Suggests: AssessORF, BiocStyle, knitr, rmarkdown
License: GPL-3
MD5sum: 5718e0a5b9fcc39902b730a27f2d799d
NeedsCompilation: no
Title: Data and Files for the AssessORF Package
Description: This package provides access to mapping and results
objects generated by the AssessORF package, as well as the
genome sequences for the strains corresponding to those
objects.
biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data,
Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data,
Genome, Proteome, SequencingData
Author: Deepank Korandla [aut], Nicholas Cooley [cre] (ORCID:
<https://orcid.org/0000-0002-6029-304X>)
Maintainer: Nicholas Cooley <npc19@pitt.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/AssessORFData
git_branch: RELEASE_3_21
git_last_commit: 309d64e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/AssessORFData_1.26.0.tar.gz
vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf
vignetteTitles: Using AssessORFData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R
suggestsMe: AssessORF
dependencyCount: 42
Package: bcellViper
Version: 1.44.0
Depends: R(>= 2.14.0), Biobase, methods
License: GPL (>=2)
MD5sum: bf9cc2294bc6e8f27f9e06ed39a6b03f
NeedsCompilation: no
Title: Human B-cell transcriptional interactome and normal human B-cell
expression data
Description: This package provides a human B-cell context-specific
transcriptional regulatory network and a human normal B-cells
dataset for the examples in package viper.
biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData
Author: Mariano Javier Alvarez
Maintainer: Mariano Javier Alvarez <malvarez@c2b2.columbia.edu>
git_url: https://git.bioconductor.org/packages/bcellViper
git_branch: RELEASE_3_21
git_last_commit: c5d0d28
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bcellViper_1.44.0.tar.gz
vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf
vignetteTitles: Using bcellViper
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R
importsMe: dorothea
suggestsMe: GenomicSuperSignature, pageRank, viper
dependencyCount: 7
Package: beadarrayExampleData
Version: 1.46.0
Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>=
2.0.0)
License: GPL-2
MD5sum: 3d6f062a348e678eec28d790878935a4
NeedsCompilation: no
Title: Example data for the beadarray package
Description: An small dataset that can be used to run examples from the
beadarray vignette and examples
biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData
Author: Mark Dunning
Maintainer: Mark Dunning <Mark.Dunning@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/beadarrayExampleData
git_branch: RELEASE_3_21
git_last_commit: 2eda649
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/beadarrayExampleData_1.46.0.tar.gz
vignettes:
vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf
vignetteTitles: beadarrayExampleData: example data for the beadarray
package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R
suggestsMe: beadarray, MiRaGE, RobLoxBioC
dependencyCount: 78
Package: BeadArrayUseCases
Version: 1.46.0
Imports: beadarray (>= 2.3.18), limma, GEOquery
Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
License: GPL-2
MD5sum: 21ad3964adb18b73f64a51bcafb848c4
NeedsCompilation: no
Title: Analysing Illumina BeadArray expression data using Bioconductor
Description: Example data files and use cases for processing Illumina
BeadArray expression data using Bioconductor
biocViews: MicroarrayData
Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie
Maintainer: Mike Smith <grimbough@gmail.com>
git_url: https://git.bioconductor.org/packages/BeadArrayUseCases
git_branch: RELEASE_3_21
git_last_commit: 7003003
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-24
source.ver: src/contrib/BeadArrayUseCases_1.46.0.tar.gz
vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf
vignetteTitles: BeadArrayUseCases.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R
dependencyCount: 108
Package: BeadSorted.Saliva.EPIC
Version: 1.16.0
Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub
Suggests: knitr, rmarkdown
License: GPL-3
MD5sum: f5923eb6219e35597eb852e3d6ed9b2a
NeedsCompilation: no
Title: Illumina EPIC data on BeadSorted child saliva cells
Description: Raw data objects used to estimate saliva cell proportion
estimates in ewastools. The FlowSorted.Saliva.EPIC object is
constructed from samples assayed by Lauren Middleton et. al.
(2021).
biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, Genome,
MethylationArrayData, ExperimentHub
Author: Jonah Fisher [aut, cre], Kelly Bakulski [aut], Lauren Middleton
[aut]
Maintainer: Jonah Fisher <jazzfish@umich.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/BeadSorted.Saliva.EPIC
git_branch: RELEASE_3_21
git_last_commit: 82df32a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.16.0.tar.gz
vignettes:
vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.html
vignetteTitles: BeadSorted.Saliva.EPIC.html
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.R
dependencyCount: 151
Package: benchmarkfdrData2019
Version: 1.21.0
Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub
Imports: utils
Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark,
dplyr, ggplot2, rlang
License: MIT + file LICENSE
MD5sum: e8a3cf73bec26133fe718b1573b0f0c2
NeedsCompilation: no
Title: Data and Benchmarking Results from Korthauer and Kimes et al.
(2019)
Description: Benchmarking results for experimental and simulated data
sets used in Korthauer and Kimes et al. (2019) to compare
methods for controlling the false discovery rate.
biocViews: SingleCellData, ExperimentData, RNASeqData, ExpressionData,
ExperimentData, ExperimentHub
Author: Stephanie Hicks [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7858-0231>), Keegan Korthauer
[aut] (ORCID: <https://orcid.org/0000-0002-4565-1654>), Patrick
Kimes [aut] (ORCID: <https://orcid.org/0000-0001-6819-9077>)
Maintainer: Stephanie Hicks <shicks19@jhu.edu>
VignetteBuilder: knitr
BugReports:
https://github.com/stephaniehicks/benchmarkfdrData2019/issues
git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019
git_branch: devel
git_last_commit: c1f2be4
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-05
source.ver: src/contrib/benchmarkfdrData2019_1.21.0.tar.gz
vignettes:
vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.html
vignetteTitles: Exploring and updating FDR benchmarking results
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.R
dependencyCount: 76
Package: beta7
Version: 1.46.0
Depends: R (>= 2.4.0), marray
License: LGPL
MD5sum: 0f6ad56ca7e5b467df69fdc5a640ca89
NeedsCompilation: no
Title: Rodriguez et al. (2004) Differential Gene Expression by
Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor
Integrin alpha4 beta7.
Description: Data from 6 gpr files aims to identify differential
expressed genes between the beta 7+ and beta 7- memory T helper
cells.
biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData
Author: Jean Yang <jean@biostat.ucsf.edu>
Maintainer: Jean Yang <jean@biostat.ucsf.edu>
git_url: https://git.bioconductor.org/packages/beta7
git_branch: RELEASE_3_21
git_last_commit: d1fcd5b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/beta7_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 8
Package: BioImageDbs
Version: 1.16.0
Depends: R (>= 4.1.0)
Imports: ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage,
magick, magrittr, filesstrings, animation, einsum
Suggests: knitr, BiocStyle, purrr
License: Artistic-2.0
MD5sum: 90dec8e0290a31dc0677fbcc502deafa
NeedsCompilation: no
Title: Bio- and biomedical imaging dataset for machine learning and
deep learning (for ExperimentHub)
Description: The package provides a bioimage dataset for the image
analysis using machine learning and deep learning. The dataset
includes microscopy imaging data with supervised labels. The
data is provided as R list data that can be loaded to
Keras/tensorflow in R.
biocViews: ExperimentHub, ExperimentData, CellCulture, Tissue
Author: Satoshi Kume [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7481-2843>), Kozo Nishida [aut]
(ORCID: <https://orcid.org/0000-0001-8501-7319>)
Maintainer: Satoshi Kume <satoshi.kume.1984@gmail.com>
URL: https://kumes.github.io/BioImageDbs/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/BioImageDbs
git_branch: RELEASE_3_21
git_last_commit: ab06d69
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/BioImageDbs_1.16.0.tar.gz
vignettes: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.html,
vignettes/BioImageDbs/inst/doc/BioImageDbs.html
vignetteTitles: The BioImageBbs Datasets, Providing Bioimage Dataset
for ExperimentHub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.R,
vignettes/BioImageDbs/inst/doc/BioImageDbs.R
dependencyCount: 102
Package: BioPlex
Version: 1.14.0
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph,
methods, utils
Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq,
ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr,
rmarkdown
License: Artistic-2.0
MD5sum: 73d2446ba1545c0a18f861d7403a445e
NeedsCompilation: no
Title: R-side access to BioPlex protein-protein interaction data
Description: The BioPlex package implements access to the BioPlex
protein-protein interaction networks and related resources from
within R. Besides protein-protein interaction networks for
HEK293 and HCT116 cells, this includes access to CORUM protein
complex data, and transcriptome and proteome data for the two
cell lines. Functionality focuses on importing the various data
resources and storing them in dedicated Bioconductor data
structures, as a foundation for integrative downstream analysis
of the data.
biocViews: CellCulture, ColonCancerData, ExperimentHub, ExpressionData,
GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome,
ReproducibleResearch, RNASeqData
Author: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut]
Maintainer: Ludwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>
URL: https://github.com/ccb-hms/BioPlex
VignetteBuilder: knitr
BugReports: https://github.com/ccb-hms/BioPlex/issues
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: RELEASE_3_21
git_last_commit: b4d955d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/BioPlex_1.14.0.tar.gz
vignettes: vignettes/BioPlex/inst/doc/BasicChecks.html,
vignettes/BioPlex/inst/doc/BioPlex.html
vignetteTitles: 2. Data checks, 1. Data retrieval
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BioPlex/inst/doc/BasicChecks.R,
vignettes/BioPlex/inst/doc/BioPlex.R
dependencyCount: 88
Package: biotmleData
Version: 1.32.0
Depends: R (>= 3.5.0)
Suggests: Biobase, SummarizedExperiment
License: file LICENSE
MD5sum: df50b56ded2201bbdc479529836360d6
NeedsCompilation: no
Title: Example experimental microarray data set for the "biotmle" R
package
Description: Microarray data (from the Illumina Ref-8 BeadChips
platform) and phenotype-level data from an epidemiological
investigation of benzene exposure, packaged using
"SummarizedExperiemnt", for use as an example with the
"biotmle" R package.
biocViews: GeneExpression, DifferentialExpression, Sequencing,
Microarray, RNASeq
Author: Nima Hejazi [aut, cre]
Maintainer: Nima Hejazi <nhejazi@berkeley.edu>
git_url: https://git.bioconductor.org/packages/biotmleData
git_branch: RELEASE_3_21
git_last_commit: cf91e5f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/biotmleData_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: biotmle
dependencyCount: 0
Package: biscuiteerData
Version: 1.22.0
Depends: R (>= 4.1.0), ExperimentHub
Imports: AnnotationHub, utils, curl, GenomicRanges
Suggests: knitr, rmarkdown, markdown
License: GPL-3
MD5sum: 6a432a3b47b30470d7684062a064d225
NeedsCompilation: no
Title: Data Package for Biscuiteer
Description: Contains default datasets used by the Bioconductor package
biscuiteer.
biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data
Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson
[aut], Jacob Morrison [aut], Lyong Heo [aut]
Maintainer: "Jacob Morrison" <jacob.morrison@vai.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/biscuiteerData
git_branch: RELEASE_3_21
git_last_commit: 1c14676
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/biscuiteerData_1.22.0.tar.gz
vignettes: vignettes/biscuiteerData/inst/doc/biscuiteerData.html
vignetteTitles: Biscuiteer User Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biscuiteerData/inst/doc/biscuiteerData.R
dependsOnMe: biscuiteer
dependencyCount: 66
Package: bladderbatch
Version: 1.46.0
Depends: Biobase
License: Artistic-2.0
MD5sum: c6db7b72946332f217d965055d44084e
NeedsCompilation: no
Title: Bladder gene expression data illustrating batch effects
Description: This package contains microarray gene expression data on
57 bladder samples from 5 batches. The data are used as an
illustrative example for the sva package.
biocViews: ExperimentData, CancerData, MicroarrayData
Author: Jeffrey T. Leek <jleek@jhsph.edu>
Maintainer: Jeffrey T. Leek <jleek@jhsph.edu>
git_url: https://git.bioconductor.org/packages/bladderbatch
git_branch: RELEASE_3_21
git_last_commit: 4545572
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bladderbatch_1.46.0.tar.gz
vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf
vignetteTitles: bladderbatchTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R
importsMe: RUVcorr
suggestsMe: BatchQC, Harman, sva
dependencyCount: 7
Package: blimaTestingData
Version: 1.28.0
Depends: R(>= 3.0.0)
Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle
License: GPL-3
MD5sum: ae2ea0226ad5a05d4a119e95cb8def97
NeedsCompilation: no
Title: Data for testing of the package blima.
Description: Experiment data package. The set were prepared using
microarray images of human mesenchymal cells treated with
various supplements. This package is intended to provide
example data to test functionality provided by blima.
biocViews: MicroarrayData, ExperimentData, GEO
Author: Vojtech Kulvait
Maintainer: Vojtech Kulvait <kulvait@gmail.com>
URL: https://bitbucket.org/kulvait/blima
git_url: https://git.bioconductor.org/packages/blimaTestingData
git_branch: RELEASE_3_21
git_last_commit: 11070ce
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/blimaTestingData_1.28.0.tar.gz
vignettes: vignettes/blimaTestingData/inst/doc/blimaTestingData.pdf
vignetteTitles: blimaTestingData.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/blimaTestingData/inst/doc/blimaTestingData.R
suggestsMe: blima
dependencyCount: 0
Package: BloodCancerMultiOmics2017
Version: 1.28.0
Depends: R (>= 3.5.0)
Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt,
broom, colorspace, cowplot, dendsort, doParallel, foreach,
forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin,
limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap,
piano, readxl, Rtsne, tidyr, xtable
License: LGPL (>= 3)
MD5sum: 5363b1c400ff0c211add0b00242538b7
NeedsCompilation: no
Title: "Drug-perturbation-based stratification of blood cancer" by
Dietrich S, OleÅ› M, Lu J et al. - experimental data and
complete analysis
Description: The package contains data of the Primary Blood Cancer
Encyclopedia (PACE) project together with a complete executable
transcript of the statistical analysis and reproduces figures
presented in the paper "Drug-perturbation-based stratification
of blood cancer" by Dietrich S, OleÅ› M, Lu J et al., J. Clin.
Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.
biocViews: ExperimentData, ReproducibleResearch, CancerData,
LeukemiaCancerData
Author: Małgorzata Oleś, Sascha Dietrich, Junyan Lu, Britta Velten,
Andreas Mock, Vladislav Kim, Wolfgang Huber
Maintainer: Małgorzata Oleś <dr.malgorzata.oles@gmail.com>
VignetteBuilder: knitr
git_url:
https://git.bioconductor.org/packages/BloodCancerMultiOmics2017
git_branch: RELEASE_3_21
git_last_commit: 4ade1ae
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/BloodCancerMultiOmics2017_1.28.0.tar.gz
vignettes:
vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.html,
vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.html
vignetteTitles: BloodCancerMultiOmics2017 - data overview,
BloodCancerMultiOmics2017
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.R,
vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.R
dependencyCount: 159
Package: bodymapRat
Version: 1.24.0
Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub
Imports: utils
Suggests: rmarkdown, knitr, BiocStyle, testthat
License: CC BY 4.0
MD5sum: 3fbb614459757d19df2691b637b77db2
NeedsCompilation: no
Title: Experimental dataset from the rat BodyMap project
Description: This package contains a SummarizedExperiment from the Yu
et al. (2013) paper that performed the rat BodyMap across 11
organs and 4 developmental stages. Raw FASTQ files were
downloaded and mapped using STAR. Data is available on
ExperimentHub as a data package.
biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData,
ExperimentHub
Author: Stephanie Hicks [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7858-0231>), Kwame Okrah [aut]
Maintainer: Stephanie Hicks <shicks19@jhu.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/bodymapRat
git_branch: RELEASE_3_21
git_last_commit: ee1600b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bodymapRat_1.24.0.tar.gz
vignettes: vignettes/bodymapRat/inst/doc/bodymapRat.html
vignetteTitles: The bodymapRat data user's guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bodymapRat/inst/doc/bodymapRat.R
suggestsMe: qsmooth
dependencyCount: 76
Package: breakpointRdata
Version: 1.26.0
Depends: R (>= 3.5)
Suggests: knitr, BiocStyle,
License: file LICENSE
MD5sum: e43189b485b38a0941a6d0db26cdeaa7
NeedsCompilation: no
Title: Strand-seq data for demonstration purposes
Description: Strand-seq data to demonstrate functionalities of
breakpointR package.
biocViews: ExperimentData, Homo_sapiens_Data, SequencingData,
DNASeqData, Genome, SingleCellData
Author: David Porubsky, Aaron Taudt, Ashley Sanders
Maintainer: David Porubsky <david.porubsky@gmail.com>
URL: https://github.com/daewoooo/breakpointRdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/breakpointRdata
git_branch: RELEASE_3_21
git_last_commit: c5e3996
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breakpointRdata_1.26.0.tar.gz
vignettes: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.pdf
vignetteTitles: Example data for breakpointR
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.R
dependsOnMe: breakpointR
dependencyCount: 0
Package: breastCancerMAINZ
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 76c0b55c5a746fceb70bd9313c3c66ea
NeedsCompilation: no
Title: Gene expression dataset published by Schmidt et al. [2008]
(MAINZ).
Description: Gene expression data from the breast cancer study
published by Schmidt et al. in 2008, provided as an eSet.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, GEO
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerMAINZ
git_branch: RELEASE_3_21
git_last_commit: 93f3f3e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerMAINZ_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: DART, genefu, MineICA
dependencyCount: 0
Package: breastCancerNKI
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: bd7374bc0937fd00a2b561b8e86fd26c
NeedsCompilation: no
Title: Genexpression dataset published by van't Veer et al. [2002] and
van de Vijver et al. [2002] (NKI).
Description: Genexpression data from a breast cancer study published by
van't Veer et al. in 2002 and van de Vijver et al. in 2002,
provided as an eSet.
biocViews: ExperimentData, CancerData, BreastCancerData, CGHData,
MicroarrayData, OneChannelData, ChipOnChipData
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerNKI
git_branch: RELEASE_3_21
git_last_commit: c0f9995
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerNKI_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, SigCheck, seventyGeneData
dependencyCount: 0
Package: breastCancerTRANSBIG
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 2bbf067f1bc029920bf6de33dbb36cc5
NeedsCompilation: no
Title: Gene expression dataset published by Desmedt et al. [2007]
(TRANSBIG).
Description: Gene expression data from a breast cancer study published
by Desmedt et al. in 2007, provided as an eSet.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, GEO
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG
git_branch: RELEASE_3_21
git_last_commit: 9d994b7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerTRANSBIG_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, GSgalgoR, MineICA
dependencyCount: 0
Package: breastCancerUNT
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 52df707d8faafa3ae7f5358087989cae
NeedsCompilation: no
Title: Gene expression dataset published by Sotiriou et al. [2007]
(UNT).
Description: Gene expression data from a breast cancer study published
by Sotiriou et al. in 2007, provided as an eSet.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, TwoChannelData, GEO
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerUNT
git_branch: RELEASE_3_21
git_last_commit: 126eb96
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerUNT_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu
dependencyCount: 0
Package: breastCancerUPP
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 5119b5f0739e8e460255d4b396ffe9f4
NeedsCompilation: no
Title: Gene expression dataset published by Miller et al. [2005] (UPP).
Description: Gene expression data from a breast cancer study published
by Miller et al. in 2005, provided as an eSet.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, GEO
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerUPP
git_branch: RELEASE_3_21
git_last_commit: 07e2ecb
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerUPP_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, GSgalgoR, MineICA, safe
dependencyCount: 0
Package: breastCancerVDX
Version: 1.46.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: e1d65698ad2cd168932d99c56fda1b5c
NeedsCompilation: no
Title: Gene expression datasets published by Wang et al. [2005] and
Minn et al. [2007] (VDX).
Description: Gene expression data from a breast cancer study published
by Wang et al. in 2005 and Minn et al. in 2007, provided as an
eSet.
biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData,
BreastCancerData, LungCancerData, MicroarrayData,
OneChannelData, GEO
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerVDX
git_branch: RELEASE_3_21
git_last_commit: fd1a1ee
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/breastCancerVDX_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: BAGS
suggestsMe: AIMS, DART, genefu, MineICA
dependencyCount: 0
Package: brgedata
Version: 1.30.0
Depends: R (>= 3.5.0), Biobase
Imports: SummarizedExperiment
Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome,
BiocStyle
License: MIT + file LICENSE
MD5sum: 0985fc1ec7bccc0045dde152bda60253
NeedsCompilation: no
Title: Exposures, Gene Expression and Methylation data for ilustration
purpouses
Description: This package contains several sets of omics data including
Gene Expression (ExpressionSet), Methylation (GenomicRatioSet),
Proteome and Exposome (ExposomeSet). This data is used in
vignettes and exaples at MEAL, MultiDataSet and omicRexposome.
biocViews:
ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData
Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut],
Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/brgedata
git_branch: RELEASE_3_21
git_last_commit: e0902bf
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/brgedata_1.30.0.tar.gz
vignettes: vignettes/brgedata/inst/doc/general_description.html
vignetteTitles: brgedata -- data R package with three omic data-set and
exposome data-set from the same Spanish pupulation
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/brgedata/inst/doc/general_description.R
suggestsMe: MEAL, MultiDataSet, omicRexposome
dependencyCount: 36
Package: bronchialIL13
Version: 1.46.0
Depends: R(>= 2.10.0), affy (>= 1.23.4)
License: GPL-2
MD5sum: 6485bade0d2080764d7b8491db104b3c
NeedsCompilation: no
Title: time course experiment involving il13
Description: derived from CNMC (pepr.cnmcresearch.org)
http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95
Human Bronchial Cell line A549
biocViews: ExperimentData, MicroarrayData
Author: Vince Carey <stvjc@channing.harvard.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL: http://www.biostat.harvard.edu/~carey
git_url: https://git.bioconductor.org/packages/bronchialIL13
git_branch: RELEASE_3_21
git_last_commit: effb992
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bronchialIL13_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 12
Package: bsseqData
Version: 0.46.0
Depends: R (>= 3.5.0), bsseq (>= 1.16.0)
License: Artistic-2.0
MD5sum: 5d5eb57faa3da3e17f4eb6d61730f4b3
NeedsCompilation: no
Title: Example whole genome bisulfite data for the bsseq package
Description: Example whole genome bisulfite data for the bsseq package
biocViews: Genome, CancerData, ColonCancerData, SequencingData
Author: Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
git_url: https://git.bioconductor.org/packages/bsseqData
git_branch: RELEASE_3_21
git_last_commit: f4f66f0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bsseqData_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: bsseq, methylSig
dependencyCount: 88
Package: bugphyzz
Version: 1.2.0
Depends: R (>= 4.4)
Imports: dplyr, utils, purrr, stringr, tidyr, tidyselect,
BiocFileCache, httr2, tools, S4Vectors
Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown,
sessioninfo, testthat, EnrichmentBrowser,
MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub,
methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle
License: Artistic-2.0
MD5sum: 8e7818f4e691f8d8aa06f8dbdedd5934
NeedsCompilation: no
Title: A harmonized data resource and software for enrichment analysis
of microbial physiologies
Description: bugphyzz is an electronic database of standardized
microbial annotations. It facilitates the creation of microbial
signatures based on shared attributes, which are utilized for
bug set enrichment analysis. The data also includes annotations
imputed with ancestra state reconstruction methods.
biocViews: MicrobiomeData, ReproducibleResearch
Author: Samuel Gamboa [aut, cre] (ORCID:
<https://orcid.org/0000-0002-6863-7943>), Levi Waldron [aut]
(ORCID: <https://orcid.org/0000-0003-2725-0694>), Kelly
Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut]
Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz@gmail.com>
URL: https://github.com/waldronlab/bugphyzz
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/bugphyzz/issues
git_url: https://git.bioconductor.org/packages/bugphyzz
git_branch: RELEASE_3_21
git_last_commit: 6e1b2a3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/bugphyzz_1.2.0.tar.gz
vignettes: vignettes/bugphyzz/inst/doc/bugphyzz.html,
vignettes/bugphyzz/inst/doc/sources.html
vignetteTitles: bugphyzz, Sources
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bugphyzz/inst/doc/bugphyzz.R,
vignettes/bugphyzz/inst/doc/sources.R
dependencyCount: 50
Package: cancerdata
Version: 1.46.0
Depends: R (>= 2.10.1), Biobase
License: GPL (>= 2)
MD5sum: b160f965596ba8d0f4443ca5b0c6eb5c
NeedsCompilation: no
Title: Development and validation of diagnostic tests from
high-dimensional molecular data: Datasets
Description: Dataset for the R package cancerclass
biocViews: CancerData, MicroarrayData
Author: Jan Budczies, Daniel Kosztyla
Maintainer: Daniel Kosztyla <danielkossi@hotmail.com>
git_url: https://git.bioconductor.org/packages/cancerdata
git_branch: RELEASE_3_21
git_last_commit: fc32f06
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/cancerdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: cancerclass
dependencyCount: 7
Package: CardinalWorkflows
Version: 1.40.0
Depends: R (>= 2.10), Cardinal, methods
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: 063749ca253fbb308771e8b094d27051
NeedsCompilation: no
Title: Datasets and workflows for the Cardinal MSI
Description: Datasets and workflows for Cardinal: DESI and MALDI
examples including pig fetus, cardinal painting, and human RCC.
biocViews: ExperimentData, MassSpectrometryData,
ImagingMassSpectrometryData
Author: Kylie A. Bemis <k.bemis@northeastern.edu>
Maintainer: Kylie A. Bemis <k.bemis@northeastern.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CardinalWorkflows
git_branch: RELEASE_3_21
git_last_commit: 10794a4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CardinalWorkflows_1.40.0.tar.gz
vignettes:
vignettes/CardinalWorkflows/inst/doc/MSI-classification.html,
vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.html,
vignettes/CardinalWorkflows/inst/doc/MSI-testing.html
vignetteTitles: 2. Classification: Supervised analysis workflow, 1.
Segmentation: Unsupervised analysis workflow, 3. Class
comparision: Statistical testing workflow
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CardinalWorkflows/inst/doc/MSI-classification.R,
vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.R,
vignettes/CardinalWorkflows/inst/doc/MSI-testing.R
dependencyCount: 67
Package: ccdata
Version: 1.34.0
Depends: R (>= 3.3)
License: MIT + file LICENSE
MD5sum: 7ff6f16174985e4dd2a41f0ce39e6013
NeedsCompilation: no
Title: Data for Combination Connectivity Mapping (ccmap) Package
Description: This package contains microarray gene expression data
generated from the Connectivity Map build 02 and LINCS l1000.
The data are used by the ccmap package to find drugs and drug
combinations to mimic or reverse a gene expression signature.
biocViews: ExperimentData, MicroarrayData, ExpressionData
Author: Alex Pickering
Maintainer: Alex Pickering <alexvpickering@gmail.com>
git_url: https://git.bioconductor.org/packages/ccdata
git_branch: RELEASE_3_21
git_last_commit: 21cb7c9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ccdata_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
importsMe: ccmap
suggestsMe: retriever
dependencyCount: 0
Package: CCl4
Version: 1.46.0
Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma
License: Artistic-2.0
MD5sum: 6eb2617dc6fc8a4226c7c92fa94bb543
NeedsCompilation: no
Title: Carbon Tetrachloride (CCl4) treated hepatocytes
Description: NChannelSet for rat hepatocytes treated with Carbon
Tetrachloride (CCl4) data from LGC company.
biocViews: ExperimentData, Genome, Rattus_norvegicus_Data,
MicroarrayData
Author: Audrey Kauffmann, Wolfgang Huber
Maintainer: Audrey Kauffmann <audrey@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/CCl4
git_branch: RELEASE_3_21
git_last_commit: 242cf87
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CCl4_1.46.0.tar.gz
vignettes: vignettes/CCl4/inst/doc/CCl4.pdf
vignetteTitles: CCl4
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CCl4/inst/doc/CCl4.R
suggestsMe: arrayQualityMetrics
dependencyCount: 10
Package: celarefData
Version: 1.26.0
Depends: R (>= 3.5.0)
Suggests: ExperimentHub, knitr, rmarkdown
License: GPL-3
MD5sum: 36f1cd3b40868798c46a0e8d6c823f3b
NeedsCompilation: no
Title: Processed scRNA data for celaref Vignette - cell labelling by
reference
Description: This experiment data contains some processed data used in
the celaref package vignette. These are publically available
datasets, that have been processed by celaref package, and can
be manipulated further with it.
biocViews: ExperimentData, SingleCellData, ExperimentHub
Author: Sarah Williams [aut, cre]
Maintainer: Sarah Williams <sarah.williams1@monash.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/celarefData
git_branch: RELEASE_3_21
git_last_commit: f6ab93a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/celarefData_1.26.0.tar.gz
vignettes: vignettes/celarefData/inst/doc/celarefData.html
vignetteTitles: Manual
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/celarefData/inst/doc/celarefData.R
dependencyCount: 0
Package: celldex
Version: 1.18.0
Depends: SummarizedExperiment
Imports: utils, methods, Matrix, ExperimentHub, AnnotationHub,
AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats,
gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI,
RSQLite, jsonlite
Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate,
BiocManager, ensembldb
License: GPL-3
MD5sum: 45f1a1f04f3b5d7adf8540c7e82021ed
NeedsCompilation: no
Title: Index of Reference Cell Type Datasets
Description: Provides a collection of reference expression datasets
with curated cell type labels, for use in procedures like
automated annotation of single-cell data or deconvolution of
bulk RNA-seq.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData
Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut],
Jared Andrews [aut], Friederike Dündar [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
URL: https://github.com/LTLA/celldex
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/
git_url: https://git.bioconductor.org/packages/celldex
git_branch: RELEASE_3_21
git_last_commit: 0a66178
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/celldex_1.18.0.tar.gz
vignettes: vignettes/celldex/inst/doc/userguide.html
vignetteTitles: Cell type references
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/celldex/inst/doc/userguide.R
dependsOnMe: OSCA.basic, OSCA.workflows, SingleRBook
importsMe: singleCellTK, scPipeline
suggestsMe: ontoProc, scDiagnostics, SingleR, sketchR,
tidySingleCellExperiment
dependencyCount: 95
Package: CellMapperData
Version: 1.34.0
Depends: ExperimentHub, CellMapper
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: c558bc073783f7959012b5e0995774de
NeedsCompilation: no
Title: Pre-processed data for use with the CellMapper package
Description: Experiment data package. Contains microarray data from
several large expression compendia that have been pre-processed
for use with the CellMapper package. This pre-processed data is
recommended for routine searches using the CellMapper package.
biocViews: ExperimentData, MicroarrayData, ExpressionData
Author: Brad Nelms
Maintainer: Brad Nelms <bnelms.research@gmail.com>
git_url: https://git.bioconductor.org/packages/CellMapperData
git_branch: RELEASE_3_21
git_last_commit: e0581fb
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CellMapperData_1.34.0.tar.gz
vignettes: vignettes/CellMapperData/inst/doc/CellMapperData.pdf
vignetteTitles: CellMapperData Introduction
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CellMapperData/inst/doc/CellMapperData.R
suggestsMe: CellMapper
dependencyCount: 66
Package: cfToolsData
Version: 1.6.0
Depends: R (>= 4.3.0)
Imports: utils, ExperimentHub
Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>=
3.0.0)
License: file LICENSE
MD5sum: da0f8d2fcbc5e62efc914335b14836ef
NeedsCompilation: no
Title: ExperimentHub data for the cfTools package
Description: The cfToolsData package supplies the data for the cfTools
package. It contains two pre-trained deep neural network (DNN)
models for the cfSort function. Additionally, it includes the
shape parameters of beta distribution characterizing
methylation markers associated with four tumor types for the
CancerDetector function, as well as the parameters
characterizing methylation markers specific to 29 primary human
tissue types for the cfDeconvolve function.
biocViews: ExperimentHub, ExperimentData, ReproducibleResearch,
DiseaseModel, CancerData, Tissue
Author: Ran Hu [aut, cre] (ORCID:
<https://orcid.org/0000-0002-0563-8957>), Shuo Li [aut] (ORCID:
<https://orcid.org/0000-0002-1960-6016>), Xianghong Jasmine
Zhou [aut] (ORCID: <https://orcid.org/0000-0002-4522-7490>),
Wenyuan Li [aut] (ORCID:
<https://orcid.org/0000-0002-5029-8525>)
Maintainer: Ran Hu <huran@ucla.edu>
URL: https://github.com/jasminezhoulab/cfToolsData
VignetteBuilder: knitr
BugReports: https://github.com/jasminezhoulab/cfToolsData/issues
git_url: https://git.bioconductor.org/packages/cfToolsData
git_branch: RELEASE_3_21
git_last_commit: e46e194
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/cfToolsData_1.6.0.tar.gz
vignettes: vignettes/cfToolsData/inst/doc/cfToolsData.html
vignetteTitles: cfToolsData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/cfToolsData/inst/doc/cfToolsData.R
importsMe: cfTools
dependencyCount: 65
Package: ChAMPdata
Version: 2.40.0
Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>=
0.16.1)
License: GPL-3
MD5sum: eaf45af0d502c702aef9bcecf35c43bf
NeedsCompilation: no
Title: Data Packages for ChAMP package
Description: Provides datasets needed for ChAMP including a test
dataset and blood controls for CNA analysis.
biocViews: ExperimentData
Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling
[ctb] and Andrew Teschendorff [ctb]
Maintainer: Yuan Tian <champ450k@gmail.com>
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_21
git_last_commit: 2e76a6e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ChAMPdata_2.40.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ChAMP, methyLImp2
dependencyCount: 23
Package: ChimpHumanBrainData
Version: 1.46.0
Depends: affy,qvalue,limma,hexbin,statmod
Suggests: hgu95av2cdf
License: MIT
MD5sum: 3b5d2dc3e999011c6ff24c108902dd1a
NeedsCompilation: no
Title: Chimp and human brain data package
Description: This data package contains chimp and human brain data
extracted from the ArrayExpress accession E-AFMX-2. Both human
and chimp RNAs were run on human hgu95av2 Affymetrix arrays.
It is a useful dataset for tutorials.
biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data,
MicroarrayData, TissueMicroarrayData, GEO
Author: Roman Jaksik, Naomi Altman, and Sean Davis
Maintainer: Sean Davis <seandavi@gmail.com>
git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData
git_branch: RELEASE_3_21
git_last_commit: a949566
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ChimpHumanBrainData_1.46.0.tar.gz
vignettes:
vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf
vignetteTitles: DiffExpressVignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R
dependencyCount: 49
Package: chipenrich.data
Version: 2.32.0
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat,
GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Drerio.UCSC.danRer10.refGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene
License: GPL-3
MD5sum: 722aa22a01cf41a5a6b195e1a9d2c6d9
NeedsCompilation: no
Title: Companion package to chipenrich
Description: Supporting data for the chipenrich package. Includes
pre-defined gene sets, gene locus definitions, and mappability
estimates.
biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment,
HistoneModification, Regression
Author: Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante
[aut], Kai Wang [cre], Laura J. Scott [ths], Maureen A. Sartor
[ths]
Maintainer: Kai Wang <wangdaha@umich.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/chipenrich.data
git_branch: RELEASE_3_21
git_last_commit: 17e3e4a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/chipenrich.data_2.32.0.tar.gz
vignettes:
vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html
vignetteTitles: chipenrich.data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R
importsMe: chipenrich
dependencyCount: 89
Package: ChIPexoQualExample
Version: 1.32.0
Depends: R (>= 3.3)
Suggests: BiocStyle, knitr, rmarkdown
License: GPL (>= 2)
MD5sum: 8ee8b68786a85320b7b4babb9f295808
NeedsCompilation: no
Title: Example data for the ChIPexoQual package, which implements a
quality control pipeline for ChIP-exo data
Description: Data for the ChIPexoQual package, consisting of (3)
chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1
in mouse liver cell lines aligned to the mm9 genome.
biocViews: ExperimentData, Genome
Author: Rene Welch, Dongjun Chung, Sunduz Keles
Maintainer: Rene Welch <welch@stat.wisc.edu>
URL: http://www.github.com/keleslab/ChIPexoQualExample
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ChIPexoQualExample
git_branch: RELEASE_3_21
git_last_commit: 352ef10
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ChIPexoQualExample_1.32.0.tar.gz
vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html
vignetteTitles: ChIPexoQualExample
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R
suggestsMe: ChIPexoQual
dependencyCount: 0
Package: chipseqDBData
Version: 1.24.0
Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors
Suggests: knitr, BiocStyle, rmarkdown
License: CC BY 4.0
MD5sum: 47d82d916eb1c5b14b336af11f9e2793
NeedsCompilation: no
Title: Data for the chipseqDB Workflow
Description: Sorted and indexed BAM files for ChIP-seq libraries, for
use in the chipseqDB workflow. BAM indices are also included.
biocViews: SequencingData, ChIPSeqData, ExperimentHub
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/chipseqDBData
git_branch: RELEASE_3_21
git_last_commit: 6726698
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/chipseqDBData_1.24.0.tar.gz
vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html
vignetteTitles: File manifest and statistics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R
dependsOnMe: csawBook
suggestsMe: chipseqDB
dependencyCount: 78
Package: ChIPXpressData
Version: 1.46.0
Depends: bigmemory
License: GPL (>=2)
MD5sum: fa0329ea015d5077bc7787a916bd2dda
NeedsCompilation: no
Title: ChIPXpress Pre-built Databases
Description: Contains pre-built mouse (GPL1261) and human (GPL570)
database of gene expression profiles to be used for ChIPXpress
ranking.
biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO
Author: George Wu
Maintainer: George Wu <gewu@jhsph.edu>
git_url: https://git.bioconductor.org/packages/ChIPXpressData
git_branch: RELEASE_3_21
git_last_commit: 9c3442c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ChIPXpressData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ChIPXpress
dependencyCount: 7
Package: chromstaRData
Version: 1.34.0
Depends: R (>= 3.3)
License: GPL-3
MD5sum: d2baf8b0ca8337242e6b646a8e8c53cc
NeedsCompilation: no
Title: ChIP-seq data for Demonstration Purposes
Description: ChIP-seq data for demonstration purposes in the chromstaR
package.
biocViews: Mus_musculus_Data, StemCell, ChIPSeqData
Author: Aaron Taudt
Maintainer: Aaron Taudt <aaron.taudt@gmail.com>
git_url: https://git.bioconductor.org/packages/chromstaRData
git_branch: RELEASE_3_21
git_last_commit: 3fce415
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/chromstaRData_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: epigraHMM
dependencyCount: 0
Package: CLL
Version: 1.48.0
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
License: LGPL
MD5sum: 70ee8ffd707e9aadf02c38039b2829d7
NeedsCompilation: no
Title: A Package for CLL Gene Expression Data
Description: The CLL package contains the chronic lymphocytic leukemia
(CLL) gene expression data. The CLL data had 24 samples that
were either classified as progressive or stable in regards to
disease progression. The data came from Dr. Sabina Chiaretti
at Division of Hematology, Department of Cellular
Biotechnologies and Hematology, University La Sapienza, Rome,
Italy and Dr. Jerome Ritz at Department of Medicine, Brigham
and Women's Hospital, Harvard Medical School, Boston,
Massachusetts.
biocViews: ExperimentData, CancerData, LeukemiaCancerData,
MicroarrayData
Author: Elizabeth Whalen
Maintainer: Robert Gentleman <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/CLL
git_branch: RELEASE_3_21
git_last_commit: b4379e8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CLL_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: phenomis
dependencyCount: 12
Package: CLLmethylation
Version: 1.28.0
Depends: R (>= 3.5.0)
Imports: SummarizedExperiment, ExperimentHub
Suggests: BiocStyle, ggplot2, knitr, rmarkdown
License: LGPL
MD5sum: 9400fc513fa2f90a470a61266915af2d
NeedsCompilation: no
Title: Methylation data of primary CLL samples in PACE project
Description: The package includes DNA methylation data for the primary
Chronic Lymphocytic Leukemia samples included in the Primary
Blood Cancer Encyclopedia (PACE) project. Raw data from the
450k DNA methylation arrays is stored in the European
Genome-Phenome Archive (EGA) under accession number
EGAS0000100174. For more information concerning the project
please refer to the paper "Drug-perturbation-based
stratification of blood cancer" by Dietrich S, Oles M, Lu J et
al., J. Clin. Invest. (2018) and R/Bioconductor package
BloodCancerMultiOmics2017.
biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData
Author: Malgorzata Oles, Andreas Mock
Maintainer: Malgorzata Oles <dr.malgorzata.oles@gmail.com>, Andreas
Mock <andreas.mock@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CLLmethylation
git_branch: RELEASE_3_21
git_last_commit: 45a78a3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CLLmethylation_1.28.0.tar.gz
vignettes: vignettes/CLLmethylation/inst/doc/CLLmethylation.html
vignetteTitles: CLLmethylation
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CLLmethylation/inst/doc/CLLmethylation.R
dependencyCount: 76
Package: CluMSIDdata
Version: 1.24.0
Depends: R (>= 3.6)
License: MIT + file LICENSE
MD5sum: 2736b7daea58d0be7cafb5835375d541
NeedsCompilation: no
Title: Data for the CluMSID package
Description: This package contains various LC-MS/MS and GC-MS data that
is used in vignettes and examples in the CluMSID package.
biocViews: ExperimentData, MassSpectrometryData
Author: Tobias Depke [aut, cre]
Maintainer: Tobias Depke <tobias.depke@helmholtz-hzi.de>
git_url: https://git.bioconductor.org/packages/CluMSIDdata
git_branch: RELEASE_3_21
git_last_commit: 0ce1ec4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CluMSIDdata_1.24.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: CluMSID
dependencyCount: 0
Package: clustifyrdatahub
Version: 1.18.0
Depends: R (>= 4.0), ExperimentHub
Imports: utils
Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr,
BiocStyle
License: MIT + file LICENSE
MD5sum: 1784e58aefe77b334e323c3b6219a252
NeedsCompilation: no
Title: External data sets for clustifyr in ExperimentHub
Description: References made from external single-cell mRNA sequencing
data sets, stored as average gene expression matrices. For use
with clustifyr <https://bioconductor.org/packages/clustifyr> to
assign cell type identities.
biocViews: SingleCellData, SequencingData, MicroarrayData,
ExperimentHub, RNASeqData, PackageTypeData, ExpressionData
Author: Rui Fu [aut] (ORCID: <https://orcid.org/0000-0001-8183-4549>),
Kent Riemondy [aut, cre] (ORCID:
<https://orcid.org/0000-0003-0750-1273>), RNA Bioscience
Initiative [fnd], Austin Gillen [ctb] (ORCID:
<https://orcid.org/0000-0003-2928-6308>), Jay Hesselberth [ctb]
(ORCID: <https://orcid.org/0000-0002-6299-179X>), Sidhant
Puntambekar [ctb]
Maintainer: Kent Riemondy <kent.riemondy@cuanschutz.edu>
URL: https://rnabioco.github.io/clustifyrdatahub/
VignetteBuilder: knitr
BugReports: https://github.com/rnabioco/clustifyrdatahub/issues
git_url: https://git.bioconductor.org/packages/clustifyrdatahub
git_branch: RELEASE_3_21
git_last_commit: cb13c46
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/clustifyrdatahub_1.18.0.tar.gz
vignettes: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.html
vignetteTitles: clustifyrdatahub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.R
dependencyCount: 65
Package: cMap2data
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 6686b2dc98b7b03d7b5419c378032736
NeedsCompilation: no
Title: Connectivity Map (version 2) Data
Description: Data package which provides default drug profiles for the
DrugVsDisease package as well as associated gene lists and data
clusters used by the DrugVsDisease package.
biocViews: Homo_sapiens_Data, MicroarrayData, GEO
Author: C. Pacini
Maintainer: J. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/cMap2data
git_branch: RELEASE_3_21
git_last_commit: ab401ed
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/cMap2data_1.44.0.tar.gz
vignettes: vignettes/cMap2data/inst/doc/cMap2data.pdf
vignetteTitles: cMap2data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cMap2data/inst/doc/cMap2data.R
dependsOnMe: DrugVsDisease
dependencyCount: 0
Package: cnvGSAdata
Version: 1.44.0
Depends: R (>= 2.10), cnvGSA
License: LGPL
MD5sum: b54162f3972209224531a6a59b459018
NeedsCompilation: no
Title: Data used in the vignette of the cnvGSA package
Description: This package contains the data used in the vignette of the
cnvGSA package.
biocViews: ExperimentData, Genome, CopyNumberVariationData
Author: Joseph Lugo <joseph.r.lugo@gmail.com>
Maintainer: Joseph Lugo <joseph.r.lugo@gmail.com>
git_url: https://git.bioconductor.org/packages/cnvGSAdata
git_branch: RELEASE_3_21
git_last_commit: ea3968f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/cnvGSAdata_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: cnvGSA
dependencyCount: 33
Package: COHCAPanno
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 56325c006a552c16653f639e83ecd6ba
NeedsCompilation: no
Title: Annotations for City of Hope CpG Island Analysis Pipeline
Description: Provides genomic location, nearby CpG island and nearby
gene information for common Illumina methylation array
platforms
biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData,
CpGIslandData, GEO, ArrayExpress
Author: Charles Warden
Maintainer: Charles Warden <cwarden45@gmail.com>
git_url: https://git.bioconductor.org/packages/COHCAPanno
git_branch: RELEASE_3_21
git_last_commit: 861cd52
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/COHCAPanno_1.44.0.tar.gz
vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf
vignetteTitles: COHCAPanno Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R
dependencyCount: 0
Package: colonCA
Version: 1.50.0
Depends: Biobase (>= 2.5.5)
License: LGPL
MD5sum: 46d932da4171e4aab85654c8e2a5c043
NeedsCompilation: no
Title: exprSet for Alon et al. (1999) colon cancer data
Description: exprSet for Alon et al. (1999) colon cancer data
biocViews: ExperimentData, Tissue, CancerData, ColonCancerData,
MicroarrayData, TissueMicroarrayData
Author: Sylvia Merk
Maintainer: W Sylvia Merk <sylvia.merk@ukmuenster.de>
git_url: https://git.bioconductor.org/packages/colonCA
git_branch: RELEASE_3_21
git_last_commit: 92f8afd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/colonCA_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: clustComp, copa
dependencyCount: 7
Package: CONFESSdata
Version: 1.36.0
Depends: R (>= 3.3)
License: GPL-2
MD5sum: 2fa34f97c7d25e3bdc83b567ab2b6609
NeedsCompilation: no
Title: Example dataset for CONFESS package
Description: Example text-converted C01 image files for use in the
CONFESS Bioconductor package.
biocViews:
HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData
Author: Diana LOW and Efthimios MOTAKIS
Maintainer: Diana LOW <dlow@imcb.a-star.edu.sg>
git_url: https://git.bioconductor.org/packages/CONFESSdata
git_branch: RELEASE_3_21
git_last_commit: 6ed9054
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CONFESSdata_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CONFESS
dependencyCount: 0
Package: ConnectivityMap
Version: 1.44.0
Depends: R (>= 2.15.1)
Suggests: RUnit, BiocGenerics
License: GPL-3
MD5sum: 187375b03cc65981ffa1846ab3fea50e
NeedsCompilation: no
Title: Functional connections between drugs, genes and diseases as
revealed by common gene-expression changes
Description: The Broad Institute's Connectivity Map (cmap02) is a
"large reference catalogue of gene-expression data from
cultured human cells perturbed with many chemicals and genetic
reagents", containing more than 7000 gene expression profiles
and 1300 small molecules.
biocViews: ExperimentData, CancerData, MicroarrayData
Author: Paul Shannon
Maintainer: Paul Shannon<pshannon@systemsbiology.org>
git_url: https://git.bioconductor.org/packages/ConnectivityMap
git_branch: RELEASE_3_21
git_last_commit: 2459a2f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ConnectivityMap_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: COPDSexualDimorphism.data
Version: 1.44.0
License: LGPL-2.1
MD5sum: 051485ca5eb8619029a2f5dc76da7025
NeedsCompilation: no
Title: Data to support sexually dimorphic and COPD differential
analysis for gene expression and methylation.
Description: Datasets to support COPDSexaulDimorphism Package.
biocViews: ExperimentData, Tissue, COPDData
Author: J Fah Sathirapongsasuti
Maintainer: J Fah Sathirapongsasuti <fah@cs.stanford.edu>
git_url:
https://git.bioconductor.org/packages/COPDSexualDimorphism.data
git_branch: RELEASE_3_21
git_last_commit: e6e8eab
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/COPDSexualDimorphism.data_1.44.0.tar.gz
vignettes: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.pdf
vignetteTitles: SDCD Genes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.R
dependencyCount: 0
Package: CopyhelpeR
Version: 1.40.0
Depends: R (>= 3.5.0)
Suggests: BiocStyle
License: GPL-2
MD5sum: abf295e3a61d73b7b508a905fca96d59
NeedsCompilation: no
Title: Helper files for CopywriteR
Description: This package contains the helper files that are required
to run the Bioconductor package CopywriteR. It contains
pre-assembled 1kb bin GC-content and mappability files for the
reference genomes hg18, hg19, hg38, mm9 and mm10. In addition,
it contains a blacklist filter to remove regions that display
CNV. Files are stored as GRanges objects from the GenomicRanges
Bioconductor package.
biocViews: Homo_sapiens, GenomicSequence
Author: Thomas Kuilman
Maintainer: Oscar Krijgsman <o.krijgsman@nki.nl>
git_url: https://git.bioconductor.org/packages/CopyhelpeR
git_branch: RELEASE_3_21
git_last_commit: 881df90
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CopyhelpeR_1.40.0.tar.gz
vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf
vignetteTitles: CopyhelpeR
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R
dependencyCount: 0
Package: CopyNeutralIMA
Version: 1.26.0
Depends: R (>= 3.5.0)
Imports: ExperimentHub,Rdpack (>= 0.8)
Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData
License: Artistic-2.0
MD5sum: 356a1eb45a5af985c93e7b82ee282d3e
NeedsCompilation: no
Title: Copy Neutral Illumina Methylation Arrays
Description: Provides a set of genomic copy neutral samples hybridized
using Illumina Methylation arrays (450k and EPIC).
biocViews:
ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO
Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut]
Maintainer: Xavier Pastor Hostench <xavier.pastor@compbio-dev.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CopyNeutralIMA
git_branch: RELEASE_3_21
git_last_commit: 052f9ff
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CopyNeutralIMA_1.26.0.tar.gz
vignettes: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.html
vignetteTitles: CopyNeutralIMA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.R
dependencyCount: 67
Package: CoSIAdata
Version: 1.8.0
Depends: R (>= 4.3.0), ExperimentHub (>= 2.6.0),
Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>=
3.7.3), knitr (>= 1.42)
License: MIT + file LICENSE
MD5sum: e1c8fd01feb108a2258f79faef34dc61
NeedsCompilation: no
Title: VST normalized RNA-Sequencing data with annotations for multiple
species samples from Bgee
Description: Variance Stabilized Transformation of Read Counts derived
from Bgee RNA-Seq Expression Data. Expression Data includes
annotations and is across 6 species (Homo sapiens, Mus
musculus, Rattus norvegicus, Danio rerio, Drosophila
melanogaster, and Caenorhabditis elegans) and across more than
132 tissues. The data is represented as a RData files and is
available in ExperimentHub.
biocViews: ExperimentHub, RNASeqData, ExperimentData, PackageTypeData,
OrganismData, Tissue,Caenorhabditis_elegans_Data,
Danio_rerio_Data, Drosophila_melanogaster_Data,
Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data,
SequencingData, ExpressionData
Author: Anisha Haldar [aut] (ORCID:
<https://orcid.org/0000-0002-1395-9793>), Vishal H. Oza [aut]
(ORCID: <https://orcid.org/0000-0001-6990-0267>), Amanda D.
Clark [cre, aut] (ORCID:
<https://orcid.org/0000-0002-1186-3114>), Nathaniel S. DeVoss
[aut] (ORCID: <https://orcid.org/0000-0003-0465-2770>),
Brittany N. Lasseigne [aut] (ORCID:
<https://orcid.org/0000-0002-1642-8904>)
Maintainer: Amanda D. Clark <amanda@freshairfamily.org>
VignetteBuilder: knitr
BugReports: https://github.com/lasseignelab/CoSIAdata/issues
git_url: https://git.bioconductor.org/packages/CoSIAdata
git_branch: RELEASE_3_21
git_last_commit: 380054f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CoSIAdata_1.8.0.tar.gz
vignettes: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.html
vignetteTitles: CoSIAdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.R
dependencyCount: 65
Package: COSMIC.67
Version: 1.44.0
Depends: R (>= 3.5.0)
Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation
Suggests: testthat, BiocStyle, knitr
License: GPL-3
MD5sum: 70666e05b47e8db5f1139b87b0676c01
NeedsCompilation: no
Title: COSMIC.67
Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version
67 (2013-10-24)
biocViews: ExperimentData, Genome, CancerData
Author: Julian Gehring
Maintainer: Julian Gehring <jg-bioc@gmx.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/COSMIC.67
git_branch: RELEASE_3_21
git_last_commit: db83c10
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/COSMIC.67_1.44.0.tar.gz
vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf
vignetteTitles: COSMIC.67 - PDF
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R
importsMe: appreci8R
dependencyCount: 79
Package: CRCL18
Version: 1.28.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: 2d4e0e64ac50e6d51180788cdeb970cb
NeedsCompilation: no
Title: CRC cell line dataset
Description: colorectal cancer mRNA and miRNA on 18 cell lines
biocViews: ExperimentData, CancerData
Author: Claudio Isella
Maintainer: Claudio Isella <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/CRCL18
git_branch: RELEASE_3_21
git_last_commit: e7ad408
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CRCL18_1.28.0.tar.gz
vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf
vignetteTitles: CRCL18
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R
dependencyCount: 7
Package: crisprScoreData
Version: 1.12.0
Depends: ExperimentHub
Imports: AnnotationHub, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat
License: MIT + file LICENSE
MD5sum: 39394b280c91b28a99321bdd5b27133b
NeedsCompilation: no
Title: Pre-trained models for the crisprScore package
Description: Provides an interface to access pre-trained models for
on-target and off-target gRNA activity prediction algorithms
implemented in the crisprScore package. Pre-trained model data
are stored in the ExperimentHub database. Users should consider
using the crisprScore package directly to use and load the
pre-trained models.
biocViews: ExperimentHub, Homo_sapiens_Data
Author: Jean-Philippe Fortin [aut, cre, cph]
Maintainer: Jean-Philippe Fortin <fortin946@gmail.com>
URL: https://github.com/crisprVerse/crisprScoreData/issues
VignetteBuilder: knitr
BugReports: https://github.com/crisprVerse/crisprScoreData
git_url: https://git.bioconductor.org/packages/crisprScoreData
git_branch: RELEASE_3_21
git_last_commit: 30e3647
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/crisprScoreData_1.12.0.tar.gz
vignettes: vignettes/crisprScoreData/inst/doc/crisprScoreData.html
vignetteTitles: crisprScoreData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/crisprScoreData/inst/doc/crisprScoreData.R
dependsOnMe: crisprScore
importsMe: crisprVerse
dependencyCount: 65
Package: curatedAdipoArray
Version: 1.20.0
Depends: R (>= 4.0)
Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment
License: GPL-3 + file LICENSE
MD5sum: 496346de768365ac967cd3a7852fc3de
NeedsCompilation: no
Title: A Curated Microarrays Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1) Under Genetic and Pharmacological
Perturbations
Description: A curated dataset of Microarrays samples. The samples are
MDI- induced pre-adipocytes (3T3-L1) at different time
points/stage of differentiation under different types of
genetic (knockdown/overexpression) and pharmacological (drug
treatment) perturbations. The package documents the data
collection and processing. In addition to the documentation,
the package contains the scripts that was used to generated the
data.
biocViews: ExperimentData, ExperimentHub, GEO, MicroarrayData
Author: Mahmoud Ahmed [aut, cre] (ORCID:
<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoArray
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoArray
git_branch: RELEASE_3_21
git_last_commit: 3495918
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedAdipoArray_1.20.0.tar.gz
vignettes: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.html
vignetteTitles: Using curatedAdipoArray
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.R
dependencyCount: 0
Package: curatedAdipoChIP
Version: 1.24.0
Depends: R (>= 3.6), SummarizedExperiment, ExperimentHub
Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi,
S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr,
tidyr, ggplot2
License: GPL-3
MD5sum: 58239d09d0f8369a3fe5fdf75a93f9d5
NeedsCompilation: no
Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1)
Description: A curated dataset of publicly available ChIP-sequencing of
transcription factors, chromatin remodelers and histone
modifications in the 3T3-L1 pre-adipocyte cell line. The
package document the data collection, pre-processing and
processing of the data. In addition to the documentation, the
package contains the scripts that was used to generated the
data.
biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData,
SequencingData
Author: Mahmoud Ahmed [aut, cre] (ORCID:
<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoChIP
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoChIP
git_branch: RELEASE_3_21
git_last_commit: 3538b4c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedAdipoChIP_1.24.0.tar.gz
vignettes: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.html
vignetteTitles: Using curatedAdipoChIP
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.R
dependencyCount: 76
Package: curatedAdipoRNA
Version: 1.24.0
Depends: R (>= 3.6), SummarizedExperiment
Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr,
dplyr, tidyr, ggplot2, S4Vectors
License: GPL-3
MD5sum: 560c54486440fec12052e2beb0009b62
NeedsCompilation: no
Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1)
Description: A curated dataset of RNA-Seq samples. The samples are
MDI-induced pre-phagocytes (3T3-L1) at different time
points/stage of differentiation. The package document the data
collection, pre-processing and processing. In addition to the
documentation, the package contains the scripts that was used
to generated the data.
biocViews: ExperimentData, GEO, RNASeqData, SequencingData
Author: Mahmoud Ahmed [aut, cre] (ORCID:
<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoRNA
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoRNA
git_branch: RELEASE_3_21
git_last_commit: 1224781
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedAdipoRNA_1.24.0.tar.gz
vignettes:
vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.html
vignetteTitles: Using curatedAdipoRNA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.R
dependencyCount: 36
Package: curatedBladderData
Version: 1.44.0
Depends: R (>= 2.10.0), affy
Suggests: BiocStyle, survival, xtable, sva, genefilter, logging
License: Artistic-2.0
MD5sum: 2f56bfb3d857f7cbb3db943762442b48
NeedsCompilation: no
Title: Bladder Cancer Gene Expression Analysis
Description: The curatedBladderData package provides relevant functions
and data for gene expression analysis in patients with bladder
cancer.
biocViews: ExperimentData, CancerData, OvarianCancerData,
MicroarrayData, ExpressionData
Author: Markus Riester
Maintainer: Markus Riester <markus@jimmy.harvard.edu>
URL: https://github.com/lima1/curatedBladderData
git_url: https://git.bioconductor.org/packages/curatedBladderData
git_branch: RELEASE_3_21
git_last_commit: 1a9065c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedBladderData_1.44.0.tar.gz
vignettes:
vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf
vignetteTitles: curatedBladderData_vignette.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R
suggestsMe: covEB
dependencyCount: 12
Package: curatedBreastData
Version: 2.36.0
Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle
Imports: methods, stats
License: GPL (>= 2)
MD5sum: c6f3f21882a252b6b5644a94b25fcf07
NeedsCompilation: no
Title: Curated breast cancer gene expression data with survival and
treatment information
Description: Curated human breast cancer tissue S4 ExpresionSet
datasets from over 16 clinical trials comprising over 2,000
patients. All datasets contain at least one type of outcomes
variable and treatment information (minimum level: whether they
had chemotherapy and whether they had hormonal therapy).
Includes code to post-process these datasets.
biocViews: ExperimentData, ExpressionData, CancerData, Tissue,
BreastCancerData, qPCRData, MicroarrayData,
TissueMicroarrayData, GEO
Author: Katie Planey
Maintainer: Katie Planey <katie.planey@gmail.com>
git_url: https://git.bioconductor.org/packages/curatedBreastData
git_branch: RELEASE_3_21
git_last_commit: 51e5733
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedBreastData_2.36.0.tar.gz
vignettes:
vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf
vignetteTitles: Manual
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R
dependencyCount: 62
Package: curatedMetagenomicData
Version: 3.16.1
Depends: R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia,
purrr, rlang, stringr, tibble, tidyr, tidyselect
Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat,
utils, uwot, vegan
License: Artistic-2.0
MD5sum: 734a77dd5c995dc4cefd813a10b7d89a
NeedsCompilation: no
Title: Curated Metagenomic Data of the Human Microbiome
Description: The curatedMetagenomicData package provides standardized,
curated human microbiome data for novel analyses. It includes
gene families, marker abundance, marker presence, pathway
abundance, pathway coverage, and relative abundance for samples
collected from different body sites. The bacterial, fungal, and
archaeal taxonomic abundances for each sample were calculated
with MetaPhlAn3, and metabolic functional potential was
calculated with HUMAnN3. The manually curated sample metadata
and standardized metagenomic data are available as
(Tree)SummarizedExperiment objects.
biocViews: ExperimentHub, Homo_sapiens_Data, MicrobiomeData,
ReproducibleResearch
Author: Lucas schiffer [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3628-0326>), Levi Waldron [aut],
Edoardo Pasolli [ctb], Jennifer Wokaty [ctb], Sean Davis [ctb],
Audrey Renson [ctb], Chloe Mirzayi [ctb], Paolo Manghi [ctb],
Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb], Valerie Obenchain
[ctb], Kelly Eckenrode [ctb], Nicola Segata [ctb]
Maintainer: Lucas schiffer <schiffer.lucas@gmail.com>
URL: https://github.com/waldronlab/curatedMetagenomicData
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues
git_url: https://git.bioconductor.org/packages/curatedMetagenomicData
git_branch: RELEASE_3_21
git_last_commit: 5e19c62
git_last_commit_date: 2025-04-18
Date/Publication: 2025-04-22
source.ver: src/contrib/curatedMetagenomicData_3.16.1.tar.gz
vignettes:
vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html
vignetteTitles: curatedMetagenomicData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R
suggestsMe: lefser, MMUPHin, OmicsMLRepoR
dependencyCount: 182
Package: curatedOvarianData
Version: 1.46.2
Depends: Biobase
Imports: BiocGenerics
Suggests: BiocStyle, futile.logger, genefilter, knitr, logging,
metafor, rmarkdown, RUnit, survival, sva, xtable
License: Artistic-2.0
MD5sum: 2f17b0ce56880a8ed908264d62a166d0
NeedsCompilation: no
Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome
Description: The curatedOvarianData package provides data for gene
expression analysis in patients with ovarian cancer.
biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData,
MicroarrayData
Author: Benjamin Ganzfried [aut], Markus Riester [aut], Steve Skates
[aut], Victoria Wang [aut], Thomas Risch [aut], Benjamin
Haibe-Kains [aut], Svitlana Tyekucheva [aut], Jie Ding [aut],
Ina Jazic [aut], Michael Birrer [aut], Giovanni Parmigiani
[aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre]
(ORCID: <https://orcid.org/0000-0003-2725-0694>)
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
URL: http://bcb.dfci.harvard.edu/ovariancancer
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/curatedOvarianData
git_branch: RELEASE_3_21
git_last_commit: c014867
git_last_commit_date: 2025-05-05
Date/Publication: 2025-05-06
source.ver: src/contrib/curatedOvarianData_1.46.2.tar.gz
vignettes:
vignettes/curatedOvarianData/inst/doc/curatedOvarianData.html
vignetteTitles: curatedOvarianData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData.R
suggestsMe: doppelgangR, TOP
dependencyCount: 7
Package: curatedPCaData
Version: 1.4.0
Depends: R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment,
RaggedExperiment
Imports: ExperimentHub, AnnotationHub, utils, methods, rlang, stats,
reshape2
Suggests: BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer,
ComplexHeatmap, corrplot, formatR
License: CC BY 4.0
MD5sum: 6518a24540d342729f0da1e274e303bd
NeedsCompilation: no
Title: Curated Prostate Cancer Data
Description: The package curatedPCaData offers a selection of annotated
prostate cancer datasets featuring multiple omics, manually
curated metadata, and derived downstream variables. The studies
are offered as MultiAssayExperiment (MAE) objects via
ExperimentHub, and comprise of clinical characteristics tied to
gene expression, copy number alteration and somatic mutation
data. Further, downstream features computed from these
multi-omics data are offered. Multiple vignettes help grasp
characteristics of the various studies and provide example
exploratory and meta-analysis of leveraging the multiple
studies provided here-in.
biocViews: ExperimentHub, ExperimentData, ProstateCancerData,
CancerData, Homo_sapiens_Data, MicroarrayData, RNASeqData,
ExpressionData, CopyNumberVariationData, Somatic, GEO,
ReproducibleResearch
Author: Teemu Daniel Laajala [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7016-7354>), Jordan Creed [ctb],
Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb],
Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael
Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
URL: https://github.com/Syksy/curatedPCaData
VignetteBuilder: knitr
BugReports: https://github.com/Syksy/curatedPCaData/issues
git_url: https://git.bioconductor.org/packages/curatedPCaData
git_branch: RELEASE_3_21
git_last_commit: bd75a85
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedPCaData_1.4.0.tar.gz
vignettes: vignettes/curatedPCaData/inst/doc/overview.html
vignetteTitles: Overview to curatedPCaData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedPCaData/inst/doc/overview.R
dependencyCount: 82
Package: curatedTBData
Version: 2.4.0
Depends: R (>= 4.3.0)
Imports: AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang,
stats
Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown,
SummarizedExperiment, sva, testthat
License: MIT + file LICENSE
MD5sum: c0946d048e5ad5b7d221609e565aad16
NeedsCompilation: no
Title: Curation of existing tuberculosis transcriptomic studies
Description: The curatedTBData is an R package that provides
standardized, curated tuberculosis(TB) transcriptomic studies.
The initial release of the package contains 49 studies. The
curatedTBData package allows users to access tuberculosis
trancriptomic efficiently and to make efficient comparison for
different TB gene signatures across multiple datasets.
biocViews: ExperimentHub, GEO, Homo_sapiens_Data
Author: Xutao Wang [aut, cre], W. Evan Johnson [aut], Prasad Patil
[aut]
Maintainer: Xutao Wang <xutaow@bu.edu>
URL: https://github.com/compbiomed/curatedTBData
VignetteBuilder: knitr
BugReports: https://github.com/compbiomed/curatedTBData/issues
git_url: https://git.bioconductor.org/packages/curatedTBData
git_branch: RELEASE_3_21
git_last_commit: 01d2f0d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedTBData_2.4.0.tar.gz
vignettes: vignettes/curatedTBData/inst/doc/curatedTBData.html
vignetteTitles: curatedTBData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/curatedTBData/inst/doc/curatedTBData.R
dependencyCount: 78
Package: curatedTCGAData
Version: 1.30.0
Depends: R (>= 4.5.0), MultiAssayExperiment
Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors,
stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
License: Artistic-2.0
MD5sum: 9a0e73e44a1dac04733380f77e2d0b6d
NeedsCompilation: no
Title: Curated Data from The Cancer Genome Atlas (TCGA) as
MultiAssayExperiment Objects
Description: This package provides publicly available data from The
Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects.
MultiAssayExperiment integrates multiple assays (e.g., RNA-seq,
copy number, mutation, microRNA, protein, and others) with
clinical / pathological data. It also links assay barcodes
with patient identifiers, enabling harmonized subsetting of
rows (features) and columns (patients / samples) across the
entire multi-'omics experiment.
biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData,
ExperimentHub
Author: Marcel Ramos [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3242-0582>), Levi Waldron [ctb],
Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie
Obenchain [ctb], Martin Morgan [ctb]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/curatedTCGAData/issues
git_url: https://git.bioconductor.org/packages/curatedTCGAData
git_branch: RELEASE_3_21
git_last_commit: 2bb3b33
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/curatedTCGAData_1.30.0.tar.gz
vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html
vignetteTitles: curatedTCGAData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R
importsMe: AMARETTO
suggestsMe: CNVRanger, dce, glmSparseNet, TCGAutils
dependencyCount: 83
Package: CytoMethIC
Version: 1.4.0
Depends: R (>= 4.4.0), ExperimentHub
Imports: utils, stats, tools, sesame, methods, sesameData,
BiocParallel, BiocManager
Suggests: tibble, BiocStyle, randomForest, testthat, knitr, rmarkdown,
e1071, xgboost, keras, tensorflow
License: Artistic-2.0
MD5sum: df37c2ef0c684c47d677a791a59f8696
NeedsCompilation: no
Title: DNA methylation-based machine learning models
Description: This package provides model data and functions for easily
using machine learning models that use data from the DNA
methylome to classify cancer type and phenotype from a sample.
The primary motivation for the development of this package is
to abstract away the granular and accessibility-limiting code
required to utilize machine learning models in R. Our package
provides this abstraction for RandomForest, e1071 Support
Vector, Extreme Gradient Boosting, and Tensorflow models. This
is paired with an ExperimentHub component, which contains
models developed for epigenetic cancer classification and
predicting phenotypes. This includes CNS tumor classification,
Pan-cancer classification, race prediction, cell of origin
classification, and subtype classification models. The package
links to our models on ExperimentHub. The package currently
supports HM450, EPIC, EPICv2, MSA, and MM285.
biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub,
MethylationArrayData, CancerData, PackageTypeData
Author: Wanding Zhou [aut] (ORCID:
<https://orcid.org/0000-0001-9126-1932>), Jacob Fanale [aut,
cre] (ORCID: <https://orcid.org/0009-0002-0490-3269>)
Maintainer: Jacob Fanale <jfanale@seas.upenn.edu>
URL: https://github.com/zhou-lab/CytoMethIC
VignetteBuilder: knitr
BugReports: https://github.com/zhou-lab/CytoMethIC/issues
git_url: https://git.bioconductor.org/packages/CytoMethIC
git_branch: RELEASE_3_21
git_last_commit: af1ed99
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/CytoMethIC_1.4.0.tar.gz
vignettes: vignettes/CytoMethIC/inst/doc/CytoMethIC.html,
vignettes/CytoMethIC/inst/doc/Oncology.html
vignetteTitles: 1. Basic Information, 2. CytoMethIC Oncology
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CytoMethIC/inst/doc/CytoMethIC.R,
vignettes/CytoMethIC/inst/doc/Oncology.R
dependencyCount: 112
Package: DAPARdata
Version: 1.38.0
Depends: R (>= 4.4.0), MSnbase
Imports: utils
Suggests: knitr, DAPAR, BiocStyle
License: GPL-2
MD5sum: 22ee1f47c5c696bcf65d7f34ea502585
NeedsCompilation: no
Title: Data accompanying the DAPAR and Prostar packages
Description: Mass-spectrometry based UPS proteomics data sets from
Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E,
Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J,
Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O,
Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic
standard dataset for testing label-free quantitative software
and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and
Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute,
Y., Burger, T. (2016). Calibration plot for proteomics: A
graphical tool to visually check the assumptions underlying FDR
control in quantitative experiments. Proteomics, 16(1), 29-32.
biocViews: ExperimentData, MassSpectrometryData, Proteome
Author: Samuel Wieczorek [cre,aut], Thomas Burger [aut], Enora Fremy
[aut]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
URL: http://www.prostar-proteomics.org/
VignetteBuilder: knitr
BugReports: https://github.com/edyp-lab/DAPARdata/issues
git_url: https://git.bioconductor.org/packages/DAPARdata
git_branch: RELEASE_3_21
git_last_commit: aa19b73
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DAPARdata_1.38.0.tar.gz
vignettes: vignettes/DAPARdata/inst/doc/dapardata.html
vignetteTitles: DAPARdata User Manual
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DAPARdata/inst/doc/dapardata.R
importsMe: DAPAR, Prostar
dependencyCount: 135
Package: davidTiling
Version: 1.48.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
License: LGPL
MD5sum: f86f047f1595dca36a0d84575bb0db98
NeedsCompilation: no
Title: Data and analysis scripts for David, Huber et al. yeast tiling
array paper
Description: This package contains the data for the paper by L. David
et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix
genechips, an ExpressionSet object with the raw feature data, a
probe annotation data structure for the chip and the yeast
genome annotation (GFF file) that was used. In addition, some
custom-written analysis functions are provided, as well as R
scripts in the scripts directory.
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data,
MicroarrayData, ReproducibleResearch
Author: Wolfgang Huber <huber@ebi.ac.uk>, Joern Toedling
<toedling@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.ebi.ac.uk/huber
git_url: https://git.bioconductor.org/packages/davidTiling
git_branch: RELEASE_3_21
git_last_commit: 8354c0c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/davidTiling_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 85
Package: depmap
Version: 1.22.0
Depends: R (>= 4.1.0), methods, dplyr
Imports: utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2,
curl, tibble
Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, stringr, tidyverse, magick
License: Artistic-2.0
MD5sum: 9b0a8236bf1c64effb3c2590435dbcd8
NeedsCompilation: no
Title: Cancer Dependency Map Data Package
Description: The depmap package is a data package that accesses datsets
from the Broad Institute DepMap cancer dependency study using
ExperimentHub. Datasets from the most current release are
available, including RNAI and CRISPR-Cas9 gene knockout screens
quantifying the genetic dependency for select cancer cell
lines. Additional datasets are also available pertaining to the
log copy number of genes for select cell lines, protein
expression of cell lines as measured by reverse phase protein
lysate microarray (RPPA), 'Transcript Per Million' (TPM) data,
as well as supplementary datasets which contain metadata and
mutation calls for the other datasets found in the current
release. The 19Q3 release adds the drug_dependency dataset,
that contains cancer cell line dependency data with respect to
drug and drug-candidate compounds. The 20Q2 release adds the
proteomic dataset that contains quantitative profiling of
proteins via mass spectrometry. This package will be updated on
a quarterly basis to incorporate the latest Broad Institute
DepMap Public cancer dependency datasets. All data made
available in this package was generated by the Broad Institute
DepMap for research purposes and not intended for clinical use.
This data is distributed under the Creative Commons license
(Attribution 4.0 International (CC BY 4.0)).
biocViews: ExperimentHub, ExperimentData, ReproducibleResearch,
RepositoryData, AssayDomainData, CopyNumberVariationData,
DiseaseModel, CancerData, BreastCancerData, ColonCancerData,
KidneyCancerData, LeukemiaCancerData, LungCancerData,
OvarianCancerData, ProstateCancerData, OrganismData,
Homo_sapiens_Data, PackageTypeData, SpecimenSource,
CellCulture, Genome, Proteome, StemCell, Tissue
Author: Laurent Gatto [cre, aut] (ORCID:
<https://orcid.org/0000-0002-1520-2268>), Theo Killian [aut],
Alexander Peltzer [ctb] (ORCID:
<https://orcid.org/0000-0002-6503-2180>)
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/depmap
git_branch: RELEASE_3_21
git_last_commit: 51c2846
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/depmap_1.22.0.tar.gz
vignettes: vignettes/depmap/inst/doc/depmap.html,
vignettes/depmap/inst/doc/using_depmap.html
vignetteTitles: depmap, depmap use cases
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/depmap/inst/doc/depmap.R,
vignettes/depmap/inst/doc/using_depmap.R
importsMe: CBNplot, DeepTarget
suggestsMe: CRISPRball, mastR, BioPlex
dependencyCount: 66
Package: derfinderData
Version: 2.26.0
Depends: R (>= 3.5.0)
Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
License: Artistic-2.0
MD5sum: 182b79504a3326f56bc47dbc460391ab
NeedsCompilation: no
Title: Processed BigWigs from BrainSpan for examples
Description: Processed 22 samples from BrainSpan keeping only the
information for chromosome 21. Data is stored in the BigWig
format and is used for examples in other packages.
biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData
Author: Leonardo Collado-Torres [aut, cre] (ORCID:
<https://orcid.org/0000-0003-2140-308X>), Andrew Jaffe [aut]
(ORCID: <https://orcid.org/0000-0001-6886-1454>), Jeffrey Leek
[aut, ths] (ORCID: <https://orcid.org/0000-0002-2873-2671>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
URL: https://github.com/leekgroup/derfinderData
VignetteBuilder: knitr
BugReports: https://github.com/leekgroup/derfinderData/issues
git_url: https://git.bioconductor.org/packages/derfinderData
git_branch: RELEASE_3_21
git_last_commit: 1b44e6b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/derfinderData_2.26.0.tar.gz
vignettes: vignettes/derfinderData/inst/doc/derfinderData.html
vignetteTitles: Introduction to derfinderData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R
suggestsMe: derfinder, derfinderPlot
dependencyCount: 0
Package: DeSousa2013
Version: 1.44.0
Depends: R (>= 2.15),
Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs,
sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr,
survival, gplots, AnnotationDbi, Biobase
License: Artistic-2.0
MD5sum: 54dc619ec0cc9f12685b6d331a67f008
NeedsCompilation: no
Title: Poor prognosis colon cancer is defined by a molecularly distinct
subtype and precursor lesion
Description: This package reproduces the main pipeline to analyze the
AMC-AJCCII-90 microarray data set in De Sousa et al. accepted
by Nature Medicine in 2013.
biocViews: CancerData, ColonCancerData, MicroarrayData
Author: Xin Wang <Xin.Wang@cruk.cam.ac.uk>
Maintainer: Xin Wang <Xin.Wang@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/DeSousa2013
git_branch: RELEASE_3_21
git_last_commit: bbc47d2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DeSousa2013_1.44.0.tar.gz
vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf
vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by
a molecular distinct subtype and develops from serrated
precursor lesions
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R
dependencyCount: 126
Package: DExMAdata
Version: 1.16.0
Depends: R (>= 4.1)
Imports: Biobase
Suggests: BiocStyle
License: GPL-2
MD5sum: 9dcb774069c3aabd3fd234b880e792fa
NeedsCompilation: no
Title: Data package for DExMA package
Description: Data objects needed to allSameID() function of DExMA
package. There are also some objects that are necessary to be
able to apply the examples of the DExMA package, which
illustrate package functionality.
biocViews: ExperimentData, OrganismData, MicroarrayData
Author: Juan Antonio Villatoro-GarcÃa [aut, cre], Pedro Carmona-Sáez
[aut]
Maintainer: Juan Antonio Villatoro-GarcÃa
<juanantoniovillatorogarcia@gmail.com>
git_url: https://git.bioconductor.org/packages/DExMAdata
git_branch: RELEASE_3_21
git_last_commit: 78b9533
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DExMAdata_1.16.0.tar.gz
vignettes: vignettes/DExMAdata/inst/doc/DExMAdata.pdf
vignetteTitles: Data for DExMA package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DExMAdata/inst/doc/DExMAdata.R
dependsOnMe: DExMA
dependencyCount: 7
Package: diffloopdata
Version: 1.36.0
Suggests: knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 9f57817675d7504bfdaf23d1957e82c1
NeedsCompilation: no
Title: Example ChIA-PET Datasets for the diffloop Package
Description: ChIA-PET example datasets and additional data for use with
the diffloop package.
biocViews: ExperimentData, SequencingData
Author: Caleb Lareau [aut], Martin Aryee [aut, cre]
Maintainer: Caleb Lareau <caleblareau@g.harvard.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/diffloopdata
git_branch: RELEASE_3_21
git_last_commit: a0b0834
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/diffloopdata_1.36.0.tar.gz
vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html
vignetteTitles: diffloopdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependencyCount: 0
Package: diggitdata
Version: 1.40.0
Depends: R(>= 2.14.0), Biobase, methods
Imports: viper
License: GPL (>=2)
MD5sum: 8c23efe5ddecc64a40166a1253b4ba0b
NeedsCompilation: no
Title: Example data for the diggit package
Description: This package provides expression profile and CNV data for
glioblastoma from TCGA, and transcriptional and
post-translational regulatory networks assembled with the
ARACNe and MINDy algorithms, respectively.
biocViews: ExperimentData, Cancer
Author: Mariano Javier Alvarez
Maintainer: Mariano Javier Alvarez <reef103@gmail.com>
git_url: https://git.bioconductor.org/packages/diggitdata
git_branch: RELEASE_3_21
git_last_commit: 4925836
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/diggitdata_1.40.0.tar.gz
vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf
vignetteTitles: Using bcellViper
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R
suggestsMe: diggit
dependencyCount: 87
Package: DLBCL
Version: 1.48.0
Depends: R(>= 2.11.0), Biobase, graph
License: GPL (>=2)
MD5sum: acb36b3ed829ed77fa2307a447b88571
NeedsCompilation: no
Title: Diffuse large B-cell lymphoma expression data
Description: This package provides additional expression data on
diffuse large B-cell lymphomas for the BioNet package.
biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich
<marcus.dittrich@biozentrum.uni-wuerzburg.de>
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
git_url: https://git.bioconductor.org/packages/DLBCL
git_branch: RELEASE_3_21
git_last_commit: 11233bc
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DLBCL_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: BioNet, mwcsr
dependencyCount: 9
Package: DMRcatedata
Version: 2.26.0
Depends: R (>= 4.0), ExperimentHub
Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Suggests: knitr
License: GPL-3
MD5sum: 16132eade6a640baaf2ef1cb3fa23dd6
NeedsCompilation: no
Title: Data Package for DMRcate
Description: This package contains 9 data objects supporting
functionality and examples of the Bioconductor package DMRcate.
biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data,
Mus_musculus_Data, SequencingData, MicroarrayData, Genome
Author: Tim Peters
Maintainer: Tim Peters <t.peters@garvan.org.au>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DMRcatedata
git_branch: RELEASE_3_21
git_last_commit: 383a0a9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DMRcatedata_2.26.0.tar.gz
vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf
vignetteTitles: The DMRcate package user's guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R
suggestsMe: DMRcate
dependencyCount: 206
Package: DNAZooData
Version: 1.8.0
Depends: R (>= 4.2), HiCExperiment
Imports: BiocFileCache, S4Vectors, rjson, utils, tools
Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: f73e6e3d315984ff56fa01eae42a4749
NeedsCompilation: no
Title: DNA Zoo data package
Description: DNAZooData is a data package giving programmatic access to
genome assemblies and Hi-C contact matrices uniformly processed
by the [DNA Zoo Consortium](https://www.dnazoo.org/). The
matrices are available in the multi-resolution `.hic` format. A
URL to corrected genome assemblies in `.fastq` format is also
provided to the end-user.
biocViews: ExperimentData, SequencingData
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
URL: https://github.com/js2264/DNAZooData
VignetteBuilder: knitr
BugReports: https://github.com/js2264/DNAZooData/issues
git_url: https://git.bioconductor.org/packages/DNAZooData
git_branch: RELEASE_3_21
git_last_commit: 8cb7246
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DNAZooData_1.8.0.tar.gz
vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html
vignetteTitles: DNAZooData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R
importsMe: OHCA
dependencyCount: 89
Package: DonaPLLP2013
Version: 1.46.0
Depends: EBImage, parallel
License: Artistic-2.0
MD5sum: fb6ea6c41a9cbde2dc191962a82f6c68
NeedsCompilation: no
Title: Supplementary data package for Dona et al. (2013) containing
example images and tables
Description: An experiment data package associated with the publication
Dona et al. (2013). Package contains runnable vignettes showing
an example image segmentation for one posterior lateral line
primordium, and also the data table and code used to analyze
tissue-scale lifetime-ratio statistics.
biocViews: ExperimentData, Tissue
Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte
Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R.
Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop,
Darren Gilmour
Maintainer: Joseph D. Barry <joseph.barry@embl.de>
git_url: https://git.bioconductor.org/packages/DonaPLLP2013
git_branch: RELEASE_3_21
git_last_commit: 204b76c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DonaPLLP2013_1.46.0.tar.gz
vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf,
vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf
vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R,
vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R
dependencyCount: 47
Package: dorothea
Version: 1.20.0
Depends: R (>= 4.0)
Imports: dplyr, magrittr, bcellViper, decoupleR,
Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap,
pkgdown, rmarkdown, Seurat, SingleCellExperiment,
SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
License: GPL-3 + file LICENSE
MD5sum: 907be6085e0119255210328cc9298b07
NeedsCompilation: no
Title: Collection Of Human And Mouse TF Regulons
Description: DoRothEA is a gene regulatory network containing signed
transcription factor (TF) - target gene interactions. DoRothEA
regulons, the collection of a TF and its transcriptional
targets, were curated and collected from different types of
evidence for both human and mouse. A confidence level was
assigned to each TF-target interaction based on the number of
supporting evidence.
biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Author: Pau Badia-i-Mompel [cre] (ORCID:
<https://orcid.org/0000-0002-1004-3923>), Daniel Dimitrov [aut]
(ORCID: <https://orcid.org/0000-0002-5197-2112>), Christian H.
Holland [aut] (ORCID: <https://orcid.org/0000-0002-3060-5786>),
Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo
Ashtiani [ctb], Attila Gabor [ctb]
Maintainer: Pau Badia-i-Mompel <pau.badia@uni-heidelberg.de>
URL: https://saezlab.github.io/dorothea/,
https://github.com/saezlab/dorothea
VignetteBuilder: knitr
BugReports: https://github.com/saezlab/dorothea/issues
git_url: https://git.bioconductor.org/packages/dorothea
git_branch: RELEASE_3_21
git_last_commit: 109bfa1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/dorothea_1.20.0.tar.gz
vignettes: vignettes/dorothea/inst/doc/dorothea.html
vignetteTitles: DoRothEA regulons.
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/dorothea/inst/doc/dorothea.R
importsMe: cosmosR, easier
suggestsMe: epiregulon.extra, MethReg
dependencyCount: 45
Package: dressCheck
Version: 0.46.0
Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5)
Suggests: survival, chron
License: Artistic-2.0
MD5sum: 341d57c31bf69f2b15eac3336f83df9e
NeedsCompilation: no
Title: data and software for checking Dressman JCO 25(5) 2007
Description: data and software for checking Dressman JCO 25(5) 2007
biocViews: ExperimentData, Genome
Author: Vincent Carey <stvjc@channing.harvard.edu>
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/dressCheck
git_branch: RELEASE_3_21
git_last_commit: 36b4f97
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/dressCheck_0.46.0.tar.gz
vignettes: vignettes/dressCheck/inst/doc/short.pdf
vignetteTitles: short review of dressCheck contents
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/dressCheck/inst/doc/short.R
dependencyCount: 7
Package: DropletTestFiles
Version: 1.18.0
Imports: utils, ExperimentHub, AnnotationHub, S4Vectors
Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils
License: GPL-3
MD5sum: 74a8641436e8336fd9b72183acc4d00f
NeedsCompilation: no
Title: Test Files for Single-Cell Droplet Utilities
Description: Assorted files generated from droplet-based single-cell
protocols, to be used for testing functions in DropletUtils.
Primarily intended for storing files that directly come out of
processing pipelines like 10X Genomics' CellRanger software,
prior to the formation of a SingleCellExperiment object. Unlike
other packages, this is not designed to provide objects that
are immediately ready for analysis.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData, SingleCellData
Author: Aaron Lun [ctb, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DropletTestFiles
git_branch: RELEASE_3_21
git_last_commit: 1a3668c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DropletTestFiles_1.18.0.tar.gz
vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html
vignetteTitles: Test files for droplet-based single-cell utilities
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R
dependsOnMe: OSCA.advanced, OSCA.intro, OSCA.workflows
suggestsMe: DropletUtils, TENxIO
dependencyCount: 65
Package: DrugVsDiseasedata
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 4ff15eb988c1a25432ee7d10eba06b1b
NeedsCompilation: no
Title: Drug versus Disease Data
Description: Data package which provides default disease expression
profiles, clusters and annotation information for use with the
DrugVsDisease package.
biocViews: Homo_sapiens_Data, MicroarrayData
Author: C. Pacini
Maintainer: J. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata
git_branch: RELEASE_3_21
git_last_commit: 54c086d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DrugVsDiseasedata_1.44.0.tar.gz
vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf
vignetteTitles: DrugVsDiseasedata
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.R
dependsOnMe: DrugVsDisease
dependencyCount: 0
Package: DuoClustering2018
Version: 1.26.0
Imports: ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
License: GPL (>=2)
MD5sum: 9aeca12067a742f419fbefcbb270868e
NeedsCompilation: no
Title: Data, Clustering Results and Visualization Functions From Duò et
al (2018)
Description: Preprocessed experimental and simulated scRNA-seq data
sets used for evaluation of clustering methods for scRNA-seq
data in Duò et al (2018). Also contains results from applying
several clustering methods to each of the data sets, and
functions for plotting method performance.
biocViews: SingleCellData, ExperimentData
Author: Angelo Duò, Charlotte Soneson
Maintainer: Angelo Duò <angelo.duo@icloud.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DuoClustering2018
git_branch: RELEASE_3_21
git_last_commit: 3f1d523
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DuoClustering2018_1.26.0.tar.gz
vignettes:
vignettes/DuoClustering2018/inst/doc/combine_data_clustering.html,
vignettes/DuoClustering2018/inst/doc/plot_performance.html,
vignettes/DuoClustering2018/inst/doc/run_clustering.html
vignetteTitles: Visualize data sets and clustering results with iSEE,
Plot performance summaries, Apply clustering method
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.R,
vignettes/DuoClustering2018/inst/doc/plot_performance.R,
vignettes/DuoClustering2018/inst/doc/run_clustering.R
suggestsMe: corral, scry
dependencyCount: 87
Package: DvDdata
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 53ca1effc24bdc72115cf462a64e1e41
NeedsCompilation: no
Title: Drug versus Disease Data
Description: Data package which provides default drug and disease
expression profiles for the DvD package.
biocViews: GEO
Author: C. Pacini
Maintainer: J. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/DvDdata
git_branch: RELEASE_3_21
git_last_commit: ba2be70
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/DvDdata_1.44.0.tar.gz
vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf
vignetteTitles: DvDdata
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DvDdata/inst/doc/DvDdata.R
dependencyCount: 0
Package: dyebiasexamples
Version: 1.48.0
Depends: R (>= 1.4.1), marray, GEOquery
Suggests: dyebias, convert, Biobase
License: GPL-3
MD5sum: 6a8856563804fc21bd023872b796a9e7
NeedsCompilation: no
Title: Example data for the dyebias package, which implements the
GASSCO method.
Description: Data for the dyebias package, consisting of 4 self-self
hybrizations of self-spotted yeast slides, as well as data from
Array Express accession E-MTAB-32
biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData,
TwoChannelData, ArrayExpress
Author: Philip Lijnzaad and Thanasis Margaritis
Maintainer: Philip Lijnzaad <plijnzaad@gmail.com>
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
git_url: https://git.bioconductor.org/packages/dyebiasexamples
git_branch: RELEASE_3_21
git_last_commit: 4661605
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/dyebiasexamples_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: dyebias
dependencyCount: 78
Package: easierData
Version: 1.14.0
Depends: R (>= 4.1.0)
Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
License: MIT + file LICENSE
MD5sum: a92e816fb082b1b4688770a58da92040
NeedsCompilation: no
Title: easier internal data and exemplary dataset from
IMvigor210CoreBiologies package
Description: Access to internal data required for the functional
performance of easier package and exemplary bladder cancer
dataset with both processed RNA-seq data and information on
response to ICB therapy generated by Mariathasan et al. "TGF-B
attenuates tumour response to PD-L1 blockade by contributing to
exclusion of T cells", published in Nature, 2018
[doi:10.1038/nature25501](https://doi.org/10.1038/nature25501).
The data is made available via
[`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/)
package under the CC-BY license.
biocViews: RNASeqData, ExperimentHub, ReproducibleResearch,
ImmunoOncologyData, CancerData, ExperimentData
Author: Oscar Lapuente-Santana [aut, cre] (ORCID:
<https://orcid.org/0000-0003-1995-8393>), Federico Marini [aut]
(ORCID: <https://orcid.org/0000-0003-3252-7758>), Arsenij
Ustjanzew [aut] (ORCID:
<https://orcid.org/0000-0002-1014-4521>), Francesca Finotello
[aut] (ORCID: <https://orcid.org/0000-0003-0712-4658>),
Federica Eduati [aut] (ORCID:
<https://orcid.org/0000-0002-7822-3867>)
Maintainer: Oscar Lapuente-Santana <o.lapuente.santana@tue.nl>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/easierData
git_branch: RELEASE_3_21
git_last_commit: 3bb83fe
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/easierData_1.14.0.tar.gz
vignettes: vignettes/easierData/inst/doc/easierData.html
vignetteTitles: easier data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/easierData/inst/doc/easierData.R
importsMe: easier
dependencyCount: 76
Package: EatonEtAlChIPseq
Version: 0.46.0
Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
License: Artistic 2.0
MD5sum: 2999ded97da6a6b686c21a1a77c9874a
NeedsCompilation: no
Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton
et al. 2010
Description: ChIP-seq analysis subset from "Conserved nucleosome
positioning defines replication origins" (PMID 20351051)
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data,
SequencingData, ChIPSeqData, GEO
Author: Patrick Aboyoun <paboyoun@fhcrc.org>
Maintainer: Patrick Aboyoun <paboyoun@fhcrc.org>
git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq
git_branch: RELEASE_3_21
git_last_commit: 01a07b9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/EatonEtAlChIPseq_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 70
Package: ecoliLeucine
Version: 1.48.0
Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf
License: GPL (>= 2)
MD5sum: 5561ef8f476c309922b57532ae316516
NeedsCompilation: no
Title: Experimental data with Affymetrix E. coli chips
Description: Experimental data with Affymetrix E. coli chips, as
reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield,
J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25,
2002
biocViews: ExperimentData, MicroarrayData
Author: Laurent Gautier
Maintainer: Laurent Gautier <lgautier@gmail.com>
git_url: https://git.bioconductor.org/packages/ecoliLeucine
git_branch: RELEASE_3_21
git_last_commit: af25ebe
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ecoliLeucine_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ecolitk
dependencyCount: 50
Package: EGSEAdata
Version: 1.36.0
Depends: R (>= 3.4)
Suggests: EGSEA
License: file LICENSE
MD5sum: 4cccea0a97382fdd3259ada84ed54a2a
NeedsCompilation: no
Title: Gene set collections for the EGSEA package
Description: This package includes gene set collections that are used
for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method
for gene set testing. It includes Human and Mouse versions of
the MSidDB (Subramanian, et al. (2005) PNAS,
102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS
Open Bio, 2:76-82) collections.
biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data,
Rattus_norvegicus_Data
Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth
Maintainer: Monther Alhamdoosh <m.hamdoosh@gmail.com>
git_url: https://git.bioconductor.org/packages/EGSEAdata
git_branch: RELEASE_3_21
git_last_commit: 800de29
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/EGSEAdata_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
importsMe: EGSEA
dependencyCount: 0
Package: ELMER.data
Version: 2.32.0
Depends: R (>= 3.5.0)
Imports: GenomicRanges
Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown
License: GPL-3
MD5sum: b71d6917ded68229d099c880e4983a1b
NeedsCompilation: no
Title: Data for the ELMER package
Description: Supporting data for the ELMER package. It includes: -
elmer.data.example.promoter: mae.promoter - elmer.data.example:
data - EPIC.hg38.manifest - EPIC.hg19.manifest -
hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table -
human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp
- Probes.motif.hg19.450K - Probes.motif.hg19.EPIC -
Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family -
TF.subfamily - Human_genes__GRCh37_p13 -
Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss -
Human_genes__GRCh38_p12__tss
biocViews: AssayDomainData, TechnologyData, OrganismData
Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P.
Berman
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ELMER.data
git_branch: RELEASE_3_21
git_last_commit: 6f55fad
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ELMER.data_2.32.0.tar.gz
vignettes: vignettes/ELMER.data/inst/doc/vignettes.html
vignetteTitles: ELMER.data: Supporting data for the ELMER package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R
dependsOnMe: ELMER
importsMe: EpiMix
dependencyCount: 23
Package: emtdata
Version: 1.16.0
Depends: R (>= 4.1)
Imports: edgeR, ExperimentHub, SummarizedExperiment
Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle,
Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
License: GPL-3
MD5sum: abee4b83d9a4bb357904cebdc1a2a6d4
NeedsCompilation: no
Title: An ExperimentHub Package for data sets with an Epithelial to
Mesenchymal Transition (EMT)
Description: This package provides pre-processed RNA-seq data where the
epithelial to mesenchymal transition was induced on cell lines.
These data come from three publications Cursons et al. (2015),
Cursons etl al. (2018) and Foroutan et al. (2017). In each of
these publications, EMT was induces across multiple cell lines
following treatment by TGFb among other stimulants. This data
will be useful in determining the regulatory programs modified
in order to achieve an EMT. Data were processed by the Davis
laboratory in the Bioinformatics division at WEHI.
biocViews: ExperimentHub, Homo_sapiens_Data, RNASeqData, ExpressionData
Author: Malvika D. Kharbanda [aut, cre] (ORCID:
<https://orcid.org/0000-0001-9726-3023>), Chin Wee Tan [aut]
(ORCID: <https://orcid.org/0000-0001-9695-7218>), Dharmesh D.
Bhuva [aut] (ORCID: <https://orcid.org/0000-0002-6398-9157>)
Maintainer: Malvika D. Kharbanda <kharbanda.m@wehi.edu.au>
URL: https://github.com/DavisLaboratory/emtdata
VignetteBuilder: knitr
BugReports: https://github.com/DavisLaboratory/emtdata/issues
git_url: https://git.bioconductor.org/packages/emtdata
git_branch: RELEASE_3_21
git_last_commit: 908e7f5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/emtdata_1.16.0.tar.gz
vignettes: vignettes/emtdata/inst/doc/emtdataR.html
vignetteTitles: emtdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/emtdata/inst/doc/emtdataR.R
dependencyCount: 80
Package: eoPredData
Version: 1.2.0
Depends: ExperimentHub
Suggests: BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics
License: MIT + file LICENSE
MD5sum: 368cf6dfe0bfaaa56cd82abb9c30db1d
NeedsCompilation: no
Title: ExperimentHub package containing model data for predicting
preeclampsia status for based on plcaental DNA methylation
profile
Description: Provides access to eoPred pretrained model hosted on
ExperimentHub. Model was trained on placental DNA methylation
preeclampsia samples using mixOmics splsda. There are two
resources: 1. the model object, and 2. a testing data set used
to demonstrate the function.
biocViews: ExperimentData, ExperimentHub, GEO, Tissue,
MethylationArrayData, Homo_sapiens_Data
Author: Iciar Boyano [aut], Victor Yuan [aut, cre]
Maintainer: Victor Yuan <victor.2wy@gmail.com>
URL: https://github.com/wvictor14/eoPredData
VignetteBuilder: knitr
BugReports: https://github.com/wvictor14/eoPredData/issues
git_url: https://git.bioconductor.org/packages/eoPredData
git_branch: RELEASE_3_21
git_last_commit: 07379be
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/eoPredData_1.2.0.tar.gz
vignettes: vignettes/eoPredData/inst/doc/eoPredData.html
vignetteTitles: eoPredData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/eoPredData/inst/doc/eoPredData.R
dependencyCount: 65
Package: EpiMix.data
Version: 1.10.0
Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6)
Suggests: rmarkdown, knitr
License: GPL-3
MD5sum: ad0cc9a17b60729d4e737e539fe364e5
NeedsCompilation: no
Title: Data for the EpiMix package
Description: Supporting data for the EpiMix R package. It include: -
HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda -
EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda -
EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData -
MET.data - mRNA.data - microRNA.data - lncRNA.data -
Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA -
Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer -
lncRNA expression data of tumors from TCGA that are stored in
the ExperimentHub.
biocViews: ExperimentData, ExperimentHub, Genome, RNASeqData,
ExpressionData
Author: Yuanning Zheng [aut, cre]
Maintainer: Yuanning Zheng <eric2021@stanford.edu>
VignetteBuilder: knitr
BugReports: https://github.com/gevaertlab/EpiMix/issues
git_url: https://git.bioconductor.org/packages/EpiMix.data
git_branch: RELEASE_3_21
git_last_commit: 14ef6c9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/EpiMix.data_1.10.0.tar.gz
vignettes: vignettes/EpiMix.data/inst/doc/RetrieveData.html
vignetteTitles: vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EpiMix.data/inst/doc/RetrieveData.R
dependsOnMe: EpiMix
dependencyCount: 65
Package: epimutacionsData
Version: 1.12.0
Depends: R (>= 4.2.0)
Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi
License: MIT + file LICENSE
MD5sum: a0994b1b960b9616af7cc133efc5bd6b
NeedsCompilation: no
Title: Data for epimutacions package
Description: This package includes the data necessary to run functions
and examples in epimutacions package. Collection of DNA
methylation data. The package contains 2 datasets: (1) Control
( GEO: GSE104812), (GEO: GSE97362) case samples; and (2)
reference panel (GEO: GSE127824). It also contains candidate
regions to be epimutations in 450k methylation arrays.
biocViews: ExperimentHub, Homo_sapiens_Data, MethylationArrayData,
MicroarrayData
Author: Leire Abarrategui [aut, cre], Juan R. Gonzalez [aut], Carlos
Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut]
Maintainer: Leire Abarrategui <abarrategui.leire@gmail.com>
URL: https://github.com/LeireAbarrategui/epimutacionsData
VignetteBuilder: knitr
BugReports: https://github.com/LeireAbarrategui/epimutacionsData/issues
git_url: https://git.bioconductor.org/packages/epimutacionsData
git_branch: RELEASE_3_21
git_last_commit: c7a24c4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/epimutacionsData_1.12.0.tar.gz
vignettes: vignettes/epimutacionsData/inst/doc/epimutacionsData.html
vignetteTitles: data repository for epimutacions package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/epimutacionsData/inst/doc/epimutacionsData.R
dependsOnMe: epimutacions
dependencyCount: 0
Package: EpipwR.data
Version: 1.2.0
Imports: ExperimentHub
Suggests: knitr, rmarkdown, sessioninfo
License: Artistic-2.0
MD5sum: 03f7549736f10c794cc570833d3a1fb3
NeedsCompilation: no
Title: EpipwR.data: Reference data for EpipwR
Description: This package provides reference data for EpipwR. EpipwR is
a fast and efficient power analysis for continuous and binary
phenotypes of epigenomic-wide association studies. This package
is only meant to be used in conjunction with EpipwR.
biocViews: ExperimentHub, MethylationArrayData, MicroarrayData,
TissueMicroarrayData, Tissue, ExperimentData
Author: Jackson Barth [aut, cre] (ORCID:
<https://orcid.org/0009-0009-6307-9928>), Austin Reynolds [aut]
Maintainer: Jackson Barth <Jackson_Barth@Baylor.edu>
URL: https://github.com/jbarth216/EpipwR.data
VignetteBuilder: knitr
BugReports: https://github.com/jbarth216/EpipwR.data
git_url: https://git.bioconductor.org/packages/EpipwR.data
git_branch: RELEASE_3_21
git_last_commit: 9c87918
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/EpipwR.data_1.2.0.tar.gz
vignettes: vignettes/EpipwR.data/inst/doc/EpipwR.data.html
vignetteTitles: EpipwR.data: Reference data for EpipwR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EpipwR.data/inst/doc/EpipwR.data.R
importsMe: EpipwR
dependencyCount: 65
Package: estrogen
Version: 1.54.0
Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter
License: LGPL
MD5sum: 6db8cf7f27f33c45ab0eb3c43a26e822
NeedsCompilation: no
Title: Microarray dataset that can be used as example for 2x2 factorial
designs
Description: Data from 8 Affymetrix genechips, looking at a 2x2
factorial design (with 2 repeats per level).
biocViews: ExperimentData, MicroarrayData
Author: Wolfgang Huber, Robert Gentleman
Maintainer: Wolfgang Huber <wolfgang.huber@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/estrogen
git_branch: RELEASE_3_21
git_last_commit: 266ae62
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/estrogen_1.54.0.tar.gz
vignettes: vignettes/estrogen/inst/doc/estrogen.pdf
vignetteTitles: estrogen
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/estrogen/inst/doc/estrogen.R
suggestsMe: categoryCompare
dependencyCount: 0
Package: etec16s
Version: 1.36.0
Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0)
License: Artistic-2.0
MD5sum: 632e8395bc6d91cd85f35c191a995ac8
NeedsCompilation: no
Title: Individual-specific changes in the human gut microbiota after
challenge with enterotoxigenic Escherichia coli and subsequent
ciprofloxacin treatment
Description: 16S rRNA gene sequencing data to study changes in the
faecal microbiota of 12 volunteers during a human challenge
study with ETEC (H10407) and subsequent treatment with
ciprofloxacin.
biocViews: ExperimentData, SequencingData, MicrobiomeData
Author: Joseph N. Paulson
Maintainer: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
git_url: https://git.bioconductor.org/packages/etec16s
git_branch: RELEASE_3_21
git_last_commit: 4987d11
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/etec16s_1.36.0.tar.gz
vignettes: vignettes/etec16s/inst/doc/etec16s.pdf
vignetteTitles: etec16s
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/etec16s/inst/doc/etec16s.R
dependencyCount: 33
Package: ewceData
Version: 1.16.0
Depends: R (>= 4.1), ExperimentHub
Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown,
testthat (>= 3.0.0)
License: Artistic-2.0
MD5sum: 4db0d7c839be0178f45d556dd8b1444e
NeedsCompilation: no
Title: The ewceData package provides reference data required for ewce
Description: This package provides reference data required for ewce.
Expression Weighted Celltype Enrichment (EWCE) is used to
determine which cell types are enriched within gene lists. The
package provides tools for testing enrichments within simple
gene lists (such as human disease associated genes) and those
resulting from differential expression studies. The package
does not depend upon any particular Single Cell Transcriptome
dataset and user defined datasets can be loaded in and used in
the analyses.
biocViews: ExperimentData, ExperimentHub, ExpressionData, Genome,
Proteome, MicroarrayData, SequencingData, SingleCellData,
RNASeqData
Author: Alan Murphy [cre] (ORCID:
<https://orcid.org/0000-0002-2487-8753>), Nathan Skene [aut]
(ORCID: <https://orcid.org/0000-0002-6807-3180>)
Maintainer: Alan Murphy <alanmurph94@hotmail.com>
URL: https://github.com/neurogenomics/ewceData
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ewceData
git_branch: RELEASE_3_21
git_last_commit: 794692e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ewceData_1.16.0.tar.gz
vignettes: vignettes/ewceData/inst/doc/ewceData.html
vignetteTitles: Data package for Expression Weighted Celltype
Enrichment EWCE
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ewceData/inst/doc/ewceData.R
importsMe: EWCE
dependencyCount: 65
Package: faahKO
Version: 1.48.1
Depends: R (>= 3.5)
Imports: xcms (>= 4.5.4)
Suggests: MSnbase (>= 2.33.3)
License: LGPL
MD5sum: b6e86772feba97b3698fbc20c3eb1559
NeedsCompilation: no
Title: Saghatelian et al. (2004) FAAH knockout LC/MS data
Description: Positive ionization mode data in NetCDF file format.
Centroided subset from 200-600 m/z and 2500-4500 seconds. Data
originally reported in "Assignment of Endogenous Substrates to
Enzymes by Global Metabolite Profiling" Biochemistry; 2004;
43(45). Also includes detected peaks in an xcmsSet.
biocViews: ExperimentData, MassSpectrometryData
Author: Colin A. Smith <csmith@scripps.edu>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
URL: http://dx.doi.org/10.1021/bi0480335
git_url: https://git.bioconductor.org/packages/faahKO
git_branch: RELEASE_3_21
git_last_commit: 15e744f
git_last_commit_date: 2025-04-23
Date/Publication: 2025-05-13
source.ver: src/contrib/faahKO_1.48.1.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: cosmiq
suggestsMe: CAMERA, IPO, MAIT, peakPantheR, xcms
dependencyCount: 143
Package: fabiaData
Version: 1.46.0
Depends: R (>= 2.10.0), Biobase
Imports: utils
Suggests: fabia
License: LGPL (>= 2.1)
MD5sum: 567a6416c2dd7190c21ab377af33eaa3
NeedsCompilation: no
Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition)
Description: Supplying gene expression data sets for the demos of the
biclustering method "Factor Analysis for Bicluster Acquisition"
(FABIA). The following three data sets are provided: A) breast
cancer (van't Veer, Nature, 2002), B) multiple tissues (Su,
PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N
Engl J Med, 2002).
biocViews: CancerData, BreastCancerData, MicroarrayData
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/fabia/fabia.html
git_url: https://git.bioconductor.org/packages/fabiaData
git_branch: RELEASE_3_21
git_last_commit: 398d13b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/fabiaData_1.46.0.tar.gz
vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf
vignetteTitles: fabiaData: Manual for the R Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R
dependencyCount: 7
Package: FANTOM3and4CAGE
Version: 1.44.0
Depends: R (>= 2.15.0)
License: GPL-3
MD5sum: 2cb1441052bf8e04e8df0781a819439b
NeedsCompilation: no
Title: CAGE data from FANTOM3 and FANTOM4 projects
Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and
FANTOM4 projects produced by RIKEN Omics Science Center.
biocViews: ExperimentData, Tissue
Author: Vanja Haberle, Department of Biology, University of Bergen,
Norway <vanja.haberle@bio.uib.no>
Maintainer: Vanja Haberle <vanja.haberle@bio.uib.no>
git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE
git_branch: RELEASE_3_21
git_last_commit: 06600b6
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FANTOM3and4CAGE_1.44.0.tar.gz
vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf
vignetteTitles: FANTOM3and4CAGE
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.R
suggestsMe: CAGEr
dependencyCount: 0
Package: ffpeExampleData
Version: 1.46.0
Depends: R (>= 2.10.0), lumi
Suggests: genefilter, affy
License: GPL (>2)
MD5sum: 11f3b5f71a1aff9718f103ebcbec2ef6
NeedsCompilation: no
Title: Illumina DASL example microarray data
Description: A subset of GSE17565 (April et al. 2009) containing 32
FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma,
with a dilution series in technical duplicate.
biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO
Author: Levi Waldron
Maintainer: Levi Waldron <lwaldron@hsph.harvard.edu>
git_url: https://git.bioconductor.org/packages/ffpeExampleData
git_branch: RELEASE_3_21
git_last_commit: 5301acf
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ffpeExampleData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ffpe
dependencyCount: 163
Package: fibroEset
Version: 1.50.0
Depends: Biobase (>= 2.5.5)
License: LGPL
MD5sum: 91ee864c62825920cc7595dc03116bf4
NeedsCompilation: no
Title: exprSet for Karaman et al. (2003) fibroblasts data
Description: exprSet for Karaman et al. (2003) human, bonobo and
gorilla fibroblasts data
biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData,
ChipOnChipData
Author: Sylvia Merk
Maintainer: Sylvia Merk <merk@ibe.med.uni-muenchen.de>
git_url: https://git.bioconductor.org/packages/fibroEset
git_branch: RELEASE_3_21
git_last_commit: f60d51e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/fibroEset_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biocGraph, clusterStab, geneplotter
dependencyCount: 7
Package: FieldEffectCrc
Version: 1.18.0
Depends: utils
Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager
License: Artistic-2.0
MD5sum: 840c0f38e7c8009a6347db1ad1f41ff1
NeedsCompilation: no
Title: Tumor, tumor-adjacent normal, and healthy colorectal
transcriptomes as SummarizedExperiment objects
Description: Processed RNA-seq data for 1,139 human primary colorectal
tissue samples across three phenotypes, including tumor, normal
adjacent-to-tumor, and healthy, available as Synapse ID
syn22237139 on synapse.org. Data have been parsed into
SummarizedExperiment objects available via ExperimentHub to
facilitate reproducibility and extension of results from
Dampier et al. (PMCID: PMC7386360, PMID: 32764205).
biocViews: ExperimentData, ReproducibleResearch, Tissue,
Homo_sapiens_Data, ColonCancerData, RNASeqData, ExpressionData,
ExperimentHub, SequencingData
Author: Christopher Dampier [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3099-6462>), Bioconductor Package
Maintainer [ctb]
Maintainer: Christopher Dampier <chd5n@virginia.edu>
URL:
http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html
VignetteBuilder: knitr
BugReports: https://github.com/Bioconductor/FieldEffectCrc/
git_url: https://git.bioconductor.org/packages/FieldEffectCrc
git_branch: RELEASE_3_21
git_last_commit: b4955ea
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FieldEffectCrc_1.18.0.tar.gz
vignettes: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.html
vignetteTitles: SummarizedExperiments of colorectal transcriptomes
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.R
dependencyCount: 118
Package: FIs
Version: 1.36.0
Depends: R (>= 3.3)
License: GPL-3
MD5sum: 65e8641d6921fd57bd7fb8cca9db1d71
NeedsCompilation: no
Title: Human Functional Interactions (FIs) for splineTimeR package
Description: Data set containing two complete lists of identified
functional interaction partners in Human. Data are derived from
Reactome and BioGRID databases.
biocViews: PathwayInteractionDatabase, Homo_sapiens_Data
Author: Agata Michna
Maintainer: Herbert Braselmann <hbraselmann@online.de>, Martin
Selmansberger <martin.selmansberger@helmholtz-muenchen.de>
git_url: https://git.bioconductor.org/packages/FIs
git_branch: RELEASE_3_21
git_last_commit: 7fcfae8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FIs_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: splineTimeR
dependencyCount: 0
Package: fission
Version: 1.28.0
Depends: R (>= 2.10), SummarizedExperiment
Suggests: knitr, markdown
License: LGPL
MD5sum: f0cc0b108093b2155e181e1060fa92d7
NeedsCompilation: no
Title: RangedSummarizedExperiment for time course RNA-Seq of fission
yeast in response to stress, by Leong et al., Nat Commun 2014.
Description: This package provides a RangedSummarizedExperiment object
of read counts in genes for a time course RNA-Seq experiment of
fission yeast (Schizosaccharomyces pombe) in response to
oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120
and 180 mins. The samples are further divided between a
wild-type group and a group with deletion of atf21. The read
count matrix was prepared and provided by the author of the
study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL,
Wilkinson CR, Miller CJ. "A global non-coding RNA system
modulates fission yeast protein levels in response to stress".
Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data,
SequencingData, RNASeqData, GEO
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/fission
git_branch: RELEASE_3_21
git_last_commit: d573663
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/fission_1.28.0.tar.gz
vignettes: vignettes/fission/inst/doc/fission.html
vignetteTitles: Fission yeast time course
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fission/inst/doc/fission.R
dependsOnMe: ROCpAI, rnaseqGene
dependencyCount: 36
Package: Fletcher2013a
Version: 1.44.0
Depends: R (>= 2.15), limma
Imports: Biobase ,VennDiagram, gplots,grid
License: GPL (>= 2)
MD5sum: 6b07145e2e6c1f052abe79bc50dd4f3c
NeedsCompilation: no
Title: Gene expression data from breast cancer cells under FGFR2
signalling perturbation
Description: The package Fletcher2013a contains time-course gene
expression data from MCF-7 cells treated under different
experimental systems in order to perturb FGFR2 signalling. The
data comes from Fletcher et al. (Nature Comms 4:2464, 2013)
where further details about the background and the experimental
design of the study can be found.
biocViews: ExperimentData, ExpressionData, CancerData,
BreastCancerData, MicroarrayData
Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin
Meyer.
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
URL: http://dx.doi.org/10.1038/ncomms3464
git_url: https://git.bioconductor.org/packages/Fletcher2013a
git_branch: RELEASE_3_21
git_last_commit: b4c9950
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Fletcher2013a_1.44.0.tar.gz
vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf
vignetteTitles: Main vignette:Fletcher2013a
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R
dependsOnMe: Fletcher2013b
suggestsMe: NetActivity
dependencyCount: 21
Package: Fletcher2013b
Version: 1.44.0
Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1),
igraph
Imports: RColorBrewer
License: GPL (>= 2)
MD5sum: 7a48e84e78f137cb2066b5cc2a5f7ab3
NeedsCompilation: no
Title: Master regulators of FGFR2 signalling and breast cancer risk
Description: This package reproduces the systems biology analysis for
the data in package Fletcher2013a using RTN.
biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData,
SNPData
Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin
Meyer.
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
URL: http://dx.doi.org/10.1038/ncomms3464
git_url: https://git.bioconductor.org/packages/Fletcher2013b
git_branch: RELEASE_3_21
git_last_commit: 6cc90dc
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Fletcher2013b_1.44.0.tar.gz
vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf
vignetteTitles: Main vignette:Fletcher2013b
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R
suggestsMe: geneplast, RTNsurvival
dependencyCount: 147
Package: flowPloidyData
Version: 1.34.0
Suggests: knitr, rmarkdown, flowCore
License: GPL-3
MD5sum: 7ba773664ce343b56de7a936881c2de7
NeedsCompilation: no
Title: Example Flow Cytometry Data
Description: A collection of raw flow cytometry data for use in
vignettes for the flowPloidy package.
biocViews: FlowCytometryData
Author: Tyler Smith <tyler@plantarum.ca>
Maintainer: Tyler Smith <tyler@plantarum.ca>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/flowPloidyData
git_branch: RELEASE_3_21
git_last_commit: bad1340
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/flowPloidyData_1.34.0.tar.gz
vignettes: vignettes/flowPloidyData/inst/doc/flowPloidyData.html
vignetteTitles: flowPloidy Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: flowPloidy
dependencyCount: 0
Package: FlowSorted.Blood.450k
Version: 1.46.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: 73a3f5c61e50105b1e33634ecebed036
NeedsCompilation: no
Title: Illumina HumanMethylation data on sorted blood cell populations
Description: Raw data objects for the Illumina 450k DNA methylation
microarrays, and an object depicting which CpGs on the array
are associated with cell type.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
TissueMicroarrayData, MethylationArrayData
Author: Andrew E Jaffe
Maintainer: Andrew E Jaffe <andrew.jaffe@libd.org>
git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k
git_branch: RELEASE_3_21
git_last_commit: 772690b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.Blood.450k_1.46.0.tar.gz
vignettes:
vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf
vignetteTitles: FlowSorted Blood 450k Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R
dependsOnMe: methylCC, methylationArrayAnalysis
suggestsMe: mCSEA, minfi, wateRmelon, FlowSorted.Blood.EPIC
dependencyCount: 144
Package: FlowSorted.Blood.EPIC
Version: 2.12.0
Depends: R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
Imports: genefilter, nlme, quadprog, graphics, stats, utils,
AnnotationHub, SummarizedExperiment, S4Vectors
Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k,
FlowSorted.Blood.450k(>= 1.0.1),
EpiDISH,FlowSorted.CordBloodNorway.450k, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Enhances: FlowSorted.CordBloodCombined.450k(>= 1.11.5)
License: GPL-3
MD5sum: 3939267df6de3aff8380babbb6084ae5
NeedsCompilation: no
Title: Illumina EPIC data on immunomagnetic sorted peripheral adult
blood cells
Description: Raw data objects to be used for blood cell proportion
estimation in minfi and similar packages. The
FlowSorted.Blood.EPIC object is based in samples assayed by
Brock Christensen and colleagues; for details see Salas et al.
2018.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
Genome, TissueMicroarrayData, MethylationArrayData
Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A.
Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb],
Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel
Hansen [ctb] (author and maintainer of the original minfi
estimateCellCounts and internal functions), Jean-Philippe
Fortin [ctb] (contributor in the original minfi
estimateCellCounts and internal functions), Shan V. Andrews
[ctb] (contributor in the original minfi estimateCellCounts and
internal functions), E. Andres Houseman [ctb] (author of the
original quadratic programming function used for cell
projection), Andrew E Jaffe [ctb] (author of the original
estimateCellCounts and internal functions within minfi)
Maintainer: Lucas A. Salas <lucas.a.salas.diaz@dartmouth.edu>
URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
VignetteBuilder: knitr
BugReports:
https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues.
git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC
git_branch: RELEASE_3_21
git_last_commit: c6e7560
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.Blood.EPIC_2.12.0.tar.gz
vignettes:
vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html
vignetteTitles: FlowSorted.Blood.EPIC
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R
importsMe: HiBED
suggestsMe: DMRcate, wateRmelon, FlowSorted.CordBloodCombined.450k
dependencyCount: 151
Package: FlowSorted.CordBlood.450k
Version: 1.36.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: 887aa1da9c61b81b583048c43117d31f
NeedsCompilation: no
Title: Illumina 450k data on sorted cord blood cells
Description: Raw data objects to be used for cord blood cell proportion
estimation in minfi.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
TissueMicroarrayData, MethylationArrayData
Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut]
Maintainer: Shan V. Andrews <sandre17@jhu.edu>
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k
git_branch: RELEASE_3_21
git_last_commit: 48e016c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.CordBlood.450k_1.36.0.tar.gz
vignettes:
vignettes/FlowSorted.CordBlood.450k/inst/doc/FlowSorted.CordBlood.450k.pdf
vignetteTitles: Minfi Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: FlowSorted.Blood.EPIC
dependencyCount: 144
Package: FlowSorted.CordBloodCombined.450k
Version: 1.24.0
Depends: R (>= 3.6), minfi (>= 1.21.2), ExperimentHub(>= 1.9.1)
Imports: SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils,
AnnotationHub
Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
License: GPL-3
MD5sum: bf4b62b5fb700df02e90a47fc18ad5e0
NeedsCompilation: no
Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells
Description: Raw data objects to be used for umbilical cord blood cell
proportion estimation in minfi and similar packages. The
FlowSorted.CordBloodCombined.450k object is based in samples
assayed by Bakulski et al, Gervin et al., de Goede et al., and
Lin et al.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
Genome, TissueMicroarrayData, MethylationArrayData,
ExperimentHub
Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C.
Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb],
John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb],
Brock C. Christensen [ctb], Janine Felix [ctb]
Maintainer: Lucas A. Salas <lucas.a.salas.diaz@dartmouth.edu>
URL:
https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k
VignetteBuilder: knitr
BugReports:
https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues.
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k
git_branch: RELEASE_3_21
git_last_commit: 0a7848a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.24.0.tar.gz
vignettes:
vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.html
vignetteTitles: FlowSorted.CordBloodCombined.450k
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.R
dependencyCount: 153
Package: FlowSorted.CordBloodNorway.450k
Version: 1.34.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: fcb39cb4efdeb324d1c4d2b5286bb372
NeedsCompilation: no
Title: Illumina HumanMethylation data on sorted cord blood cell
populations
Description: Raw data objects for the Illumina 450k DNA methylation
microarrays, for cell type composition estimation.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
TissueMicroarrayData, MethylationArrayData
Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut]
Maintainer: kristina gervin <kristina.gervin@medisin.uio.no>
URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k
git_branch: RELEASE_3_21
git_last_commit: 95eacd1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 144
Package: FlowSorted.DLPFC.450k
Version: 1.44.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: aa1b99d81c2aece8b6ef8261e44c6616
NeedsCompilation: no
Title: Illumina HumanMethylation data on sorted frontal cortex cell
populations
Description: Raw data objects for the Illumina 450k DNA methylation
microarrays.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
TissueMicroarrayData, MethylationArrayData
Author: Andrew E Jaffe, Zachary A. Kaminsky
Maintainer: Andrew E Jaffe <andrew.jaffe@libd.org>
git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k
git_branch: RELEASE_3_21
git_last_commit: b6d17ff
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/FlowSorted.DLPFC.450k_1.44.0.tar.gz
vignettes:
vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf
vignetteTitles: FlowSorted DLPFC 450k Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R
importsMe: HiBED
dependencyCount: 144
Package: flowWorkspaceData
Version: 3.20.0
License: GPL-2
MD5sum: 1ecd3bd13070d38b09b8cdb45c165d94
NeedsCompilation: no
Title: A data package containing two flowJo, one diva xml workspace and
the associated fcs files as well as three GatingSets for
testing the flowWorkspace, openCyto and CytoML packages.
Description: The necessary external data to run the flowWorkspace and
openCyto vignette is found in this package.
biocViews: ExperimentData, FlowCytometryData
Author: Greg Finak
Maintainer: Mike Jiang <wjiang2@fhcrc.org>
git_url: https://git.bioconductor.org/packages/flowWorkspaceData
git_branch: RELEASE_3_21
git_last_commit: c3d7b13
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/flowWorkspaceData_3.20.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace,
ggcyto, openCyto
dependencyCount: 0
Package: fourDNData
Version: 1.8.0
Depends: R (>= 4.2)
Imports: BiocFileCache, HiCExperiment, GenomicRanges, IRanges,
S4Vectors, utils, tools
Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr,
rmarkdown
License: MIT + file LICENSE
MD5sum: f9b6327e4df83e5d00297e8b7e50b021
NeedsCompilation: no
Title: 4DN data package
Description: fourDNData is a data package giving programmatic access to
Hi-C contact matrices uniformly processed by the [4DN
consortium](https://www.4dnucleome.org/). The matrices are
available in the multi-resolution `.mcool` format.
biocViews: ExperimentData, SequencingData
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
URL: https://github.com/js2264/fourDNData
VignetteBuilder: knitr
BugReports: https://github.com/js2264/fourDNData/issues
git_url: https://git.bioconductor.org/packages/fourDNData
git_branch: RELEASE_3_21
git_last_commit: 79cb8b4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/fourDNData_1.8.0.tar.gz
vignettes: vignettes/fourDNData/inst/doc/fourDNData.html
vignetteTitles: fourDNData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R
importsMe: OHCA
dependencyCount: 88
Package: frmaExampleData
Version: 1.44.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 0e053530cddde46811ef320315070711
NeedsCompilation: no
Title: Frma Example Data
Description: Data files used by the examples in frma and frmaTools
packages
biocViews: Homo_sapiens_Data, MicroarrayData
Author: Matthew N. McCall <mmccall@jhsph.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/frmaExampleData
git_branch: RELEASE_3_21
git_last_commit: aefb4d9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/frmaExampleData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: frma, frmaTools
dependencyCount: 0
Package: furrowSeg
Version: 1.36.0
Depends: R (>= 3.3), EBImage
Imports: abind, dplyr, locfit, tiff
Suggests: BiocStyle, ggplot2, knitr
License: Artistic-2.0
MD5sum: cd48069ebb09c9d6cae61677e0a6aad7
NeedsCompilation: no
Title: Furrow Segmentation
Description: Image feature data and analysis codes for the Guglielmi,
Barry et al. paper describing the application of an
optogenetics tools to disrupt Drosophila embryo furrowing.
biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue,
ReproducibleResearch
Author: Joseph Barry
Maintainer: Joseph Barry <joseph.barry@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/furrowSeg
git_branch: RELEASE_3_21
git_last_commit: 65d9e3b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/furrowSeg_1.36.0.tar.gz
vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf,
vignettes/furrowSeg/inst/doc/genPaperFigures.pdf
vignetteTitles: Supplementary Methods - Example furrow segmentation,
Supplementary Methods - Automatic generation of paper figures
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R,
vignettes/furrowSeg/inst/doc/genPaperFigures.R
dependencyCount: 55
Package: gageData
Version: 2.46.0
Depends: R (>= 2.10)
Suggests: gage, pathview, genefilter
License: GPL (>=2.0)
MD5sum: 15cdfd337b39e35b3eefdf4b0671a9de
NeedsCompilation: no
Title: Auxillary data for gage package
Description: This is a supportive data package for the software
package, gage. However, the data supplied here are also useful
for gene set or pathway analysis or microarray data analysis in
general. In this package, we provide two demo microarray
dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6
(originally published as an demo dataset for GAGE, also
registered as GSE13604 in GEO). This package also includes
commonly used gene set data based on KEGG pathways and GO terms
for major research species, including human, mouse, rat and
budding yeast. Mapping data between common gene IDs for budding
yeast are also included.
biocViews: ExperimentData, StemCell, CancerData, BreastCancerData,
MicroarrayData, GEO
Author: Weijun Luo
Maintainer: Weijun Luo <luo_weijun@yahoo.com>
git_url: https://git.bioconductor.org/packages/gageData
git_branch: RELEASE_3_21
git_last_commit: 79fb681
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gageData_2.46.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: gage
dependencyCount: 0
Package: gaschYHS
Version: 1.46.0
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: 26f4a9f1aa5c568b77811cc9bae33692
NeedsCompilation: no
Title: ExpressionSet for response of yeast to heat shock and other
environmental stresses
Description: Data from PMID 11102521
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data
Author: Audrey Gasch and colleagues
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL:
http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt
git_url: https://git.bioconductor.org/packages/gaschYHS
git_branch: RELEASE_3_21
git_last_commit: 9400876
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gaschYHS_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 7
Package: gcspikelite
Version: 1.46.0
Depends: R (>= 2.5.0)
License: LGPL
MD5sum: 2b763d12fd7f405c2f3bf395c8b47746
NeedsCompilation: no
Title: Spike-in data for GC/MS data and methods within flagme
Description: Spike-in data for GC/MS data and methods within flagme
biocViews: MassSpectrometryData
Author: Mark Robinson <mrobinson@wehi.edu.au>
Maintainer: Mark Robinson <mrobinson@wehi.edu.au>
git_url: https://git.bioconductor.org/packages/gcspikelite
git_branch: RELEASE_3_21
git_last_commit: 434621a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gcspikelite_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: flagme
suggestsMe: erah
dependencyCount: 0
Package: gDNAinRNAseqData
Version: 1.8.0
Depends: R (>= 4.3)
Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: be4ed4c434e96c5007fb4d8dfa53b65c
NeedsCompilation: no
Title: RNA-seq data with different levels of gDNA contamination
Description: Provides access to BAM files generated from RNA-seq data
produced with different levels of gDNA contamination. It
currently allows one to download a subset of the data published
by Li et al., BMC Genomics, 23:554, 2022. This subset of data
is formed by BAM files with about 100,000 alignments with three
different levels of gDNA contamination.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData, Homo_sapiens_Data
Author: Robert Castelo [aut, cre] (ORCID:
<https://orcid.org/0000-0003-2229-4508>)
Maintainer: Robert Castelo <robert.castelo@upf.edu>
URL: https://github.com/functionalgenomics/gDNAinRNAseqData
VignetteBuilder: knitr
BugReports: https://github.com/functionalgenomics/gDNAinRNAseqData
git_url: https://git.bioconductor.org/packages/gDNAinRNAseqData
git_branch: RELEASE_3_21
git_last_commit: 4c8ebbd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gDNAinRNAseqData_1.8.0.tar.gz
vignettes: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.html
vignetteTitles: RNA-seq data with different levels of gDNA
contamination
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.R
suggestsMe: gDNAx
dependencyCount: 80
Package: gDRtestData
Version: 1.6.0
Depends: R (>= 4.2)
Imports: checkmate, data.table
Suggests: BiocStyle, gDRstyle (>= 1.1.5), knitr, qs, reshape2,
rmarkdown, SummarizedExperiment, testthat, yaml
License: Artistic-2.0
MD5sum: ed97d9c840f3e6380009128d576d3cbe
NeedsCompilation: no
Title: gDRtestData - R data package with testing dose response data
Description: R package with internal dose-response test data. Package
provides functions to generate input testing data that can be
used as the input for gDR pipeline. It also contains qs files
with MAE data processed by gDR.
biocViews: ExperimentData, TechnologyData
Author: Aleksander Chlebowski [aut], Bartosz Czech [aut] (ORCID:
<https://orcid.org/0000-0002-9908-3007>), Arkadiusz Gladki
[cre, aut] (ORCID: <https://orcid.org/0000-0002-7059-6378>),
Marc Hafner [aut] (ORCID:
<https://orcid.org/0000-0003-1337-7598>), Marcin Kamianowski
[aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz
Scigocki [aut], Janina Smola [aut], Allison Voung [aut]
Maintainer: Arkadiusz Gladki <gladki.arkadiusz@gmail.com>
URL: https://github.com/gdrplatform/gDRtestData,
https://gdrplatform.github.io/gDRtestData/
VignetteBuilder: knitr
BugReports: https://github.com/gdrplatform/gDRtestData/issues
git_url: https://git.bioconductor.org/packages/gDRtestData
git_branch: RELEASE_3_21
git_last_commit: 5ede591
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gDRtestData_1.6.0.tar.gz
vignettes: vignettes/gDRtestData/inst/doc/gDRtestData.html
vignetteTitles: gDRtestData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gDRtestData/inst/doc/gDRtestData.R
suggestsMe: gDR, gDRcore, gDRimport, gDRutils
dependencyCount: 5
Package: geneLenDataBase
Version: 1.44.0
Depends: R (>= 2.11.0)
Imports: utils, rtracklayer, GenomicFeatures, txdbmaker
License: LGPL (>= 2)
MD5sum: e1460da5a597ce80521505e1e8087b8c
NeedsCompilation: no
Title: Lengths of mRNA transcripts for a number of genomes
Description: Length of mRNA transcripts for a number of genomes and
gene ID formats, largely based on UCSC table browser. Data
objects are provided as individual pieces of information to be
retrieved and loaded. A variety of different gene identifiers
and genomes is supported to ensure wide applicability.
biocViews: ExperimentData, Genome
Author: Matthew Young [aut], Nadia Davidson [aut], Federico Marini
[ctb, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <marinif@uni-mainz.de>
URL: https://github.com/federicomarini/geneLenDataBase
BugReports: https://github.com/federicomarini/geneLenDataBase/issues
git_url: https://git.bioconductor.org/packages/geneLenDataBase
git_branch: RELEASE_3_21
git_last_commit: ad5f383
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/geneLenDataBase_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: goseq
importsMe: SMITE
dependencyCount: 100
Package: genomationData
Version: 1.40.0
Suggests: knitr
License: GPL-3
MD5sum: 92c84a22e6220ffcd579e136195676c8
NeedsCompilation: no
Title: Experimental data for showing functionalities of the genomation
package
Description: The package contains Chip Seq, Methylation and Cage data,
downloaded from Encode
biocViews: ExperimentData, Genome, StemCell, SequencingData,
ChIPSeqData, ChipOnChipData, ENCODE
Author: Altuna Akalin, Vedran Franke
Maintainer: Vedran Franke <vedran.franke@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/genomationData
git_branch: RELEASE_3_21
git_last_commit: cbaf864
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/genomationData_1.40.0.tar.gz
vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf
vignetteTitles: genomationData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genomationData/inst/doc/genomationData-knitr.R
suggestsMe: genomation
dependencyCount: 0
Package: GenomicDistributionsData
Version: 1.16.0
Depends: R (>= 4.1)
Imports: ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter,
data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ensembldb
Suggests: knitr, BiocStyle, rmarkdown
License: BSD_2_clause + file LICENSE
MD5sum: eb4257df6ca45bfec77e850d737b3e0a
NeedsCompilation: no
Title: Reference data for GenomicDistributions package
Description: This package provides ready to use reference data for
GenomicDistributions package. Raw data was obtained from
ensembldb and processed with helper functions. Data files are
available for the following genome assemblies: hg19, hg38, mm9
and mm10.
biocViews: ExperimentHub, ExperimentData, Genome
Author: Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose
Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan
C. Sheffield [ctb]
Maintainer: Kristyna Kupkova <kristynakupkova@gmail.com>
VignetteBuilder: knitr
BugReports: http://github.com/databio/GenomicDistributionsData
git_url: https://git.bioconductor.org/packages/GenomicDistributionsData
git_branch: RELEASE_3_21
git_last_commit: d73e4b4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GenomicDistributionsData_1.16.0.tar.gz
vignettes: vignettes/GenomicDistributionsData/inst/doc/intro.html
vignetteTitles: 1. Getting started with GenomicDistributionsData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GenomicDistributionsData/inst/doc/intro.R
suggestsMe: GenomicDistributions
dependencyCount: 102
Package: GeuvadisTranscriptExpr
Version: 1.36.0
Depends: R (>= 3.5.0)
Suggests: limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
License: GPL (>= 3)
MD5sum: 97d1fd046c746c913385c07d1512f4ef
NeedsCompilation: no
Title: Data package with transcript expression and bi-allelic genotypes
from the GEUVADIS project
Description: Provides transcript expression and bi-allelic genotypes
corresponding to the chromosome 19 for CEU individuals from the
GEUVADIS project, Lappalainen et al.
biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData,
SequencingData, ExpressionData
Author: Malgorzata Nowicka [aut, cre]
Maintainer: Malgorzata Nowicka <gosia.nowicka@uzh.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr
git_branch: RELEASE_3_21
git_last_commit: 2a8d54d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GeuvadisTranscriptExpr_1.36.0.tar.gz
vignettes:
vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.pdf
vignetteTitles: Preprocessing and preparation of transcript expression
and genotypes from the GEUVADIS project for sQTL analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.R
suggestsMe: DRIMSeq
dependencyCount: 0
Package: GIGSEAdata
Version: 1.26.0
Depends: R (>= 3.5)
Suggests: GIGSEA, knitr, rmarkdown
License: LGPL-3
MD5sum: 4e94abe7151b807e373214d5d169ee7e
NeedsCompilation: no
Title: Gene set collections for the GIGSEA package
Description: The gene set collection used for the GIGSEA package.
biocViews: ExperimentData, Homo_sapiens_Data
Author: Shijia Zhu
Maintainer: Shijia Zhu <shijia.zhu@mssm.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GIGSEAdata
git_branch: RELEASE_3_21
git_last_commit: 4e9bfb3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GIGSEAdata_1.26.0.tar.gz
vignettes: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.pdf
vignetteTitles: GIGSEAdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.R
dependencyCount: 0
Package: golubEsets
Version: 1.50.0
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
License: LGPL
MD5sum: 6b2008cc60740ef52c6900fcea9f8f3d
NeedsCompilation: no
Title: exprSets for golub leukemia data
Description: representation of public golub data with some covariate
data of provenance unknown to the maintainer at present; now
employs ExpressionSet format
biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData
Author: Todd Golub <golub@wi.mit.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/golubEsets
git_branch: RELEASE_3_21
git_last_commit: 9ab1c6b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/golubEsets_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest,
idiogram, MLInterfaces, pvca, RDRToolbox, twilight
dependencyCount: 7
Package: gpaExample
Version: 1.20.0
Depends: R (>= 4.0.0)
License: GPL (>= 2)
MD5sum: 8ebf4f07fd178f314e00a596213d4dca
NeedsCompilation: no
Title: Example data for the GPA package (Genetic analysis incorporating
Pleiotropy and Annotation)
Description: Example data for the GPA package, consisting of the
p-values of 1,219,805 SNPs for five psychiatric disorder GWAS
from the psychiatric GWAS consortium (PGC), with the annotation
data using genes preferentially expressed in the central
nervous system (CNS).
biocViews: ExperimentData, Homo_sapiens_Data, SNPData
Author: Dongjun Chung, Carter Allen
Maintainer: Dongjun Chung <dongjun.chung@gmail.com>
URL: http://dongjunchung.github.io/GPA/
git_url: https://git.bioconductor.org/packages/gpaExample
git_branch: RELEASE_3_21
git_last_commit: bf1e5ac
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/gpaExample_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GPA
dependencyCount: 0
Package: grndata
Version: 1.40.0
Depends: R (>= 2.10)
Suggests: RUnit, BiocGenerics, knitr
License: GPL-3
MD5sum: 6240852596c3d90613c6db55356bb40a
NeedsCompilation: no
Title: Synthetic Expression Data for Gene Regulatory Network Inference
Description: Simulated expression data for five large Gene Regulatory
Networks from different simulators
biocViews: ExperimentData, NetworkInference, GeneExpression,
Microarray, GeneRegulation, Network
Author: Pau Bellot, Catharina Olsen, Patrick E Meyer
Maintainer: Pau Bellot <pau.bellot@upc.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/grndata
git_branch: RELEASE_3_21
git_last_commit: 19ea80c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/grndata_1.40.0.tar.gz
vignettes: vignettes/grndata/inst/doc/grndata.html
vignetteTitles: GRNdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: GSBenchMark
Version: 1.28.0
Depends: R (>= 2.13.1)
License: GPL-2
MD5sum: 09a9bfcd03e244846dcc50222cd0edea
NeedsCompilation: no
Title: Gene Set Benchmark
Description: Benchmarks for Machine Learning Analysis of the Gene Sets.
The package contains a list of pathways and gene expression
data sets used in "Identifying Tightly Regulated and Variably
Expressed Networks by Differential Rank Conservation (DIRAC)"
(2010) by Eddy et al.
biocViews: MicroarrayData
Author: Bahman Afsari <bahman@jhu.edu>, Elana J. Fertig
<ejfertig@jhmi.edu>
Maintainer: Bahman Afsari <bahman@jhu.edu>
git_url: https://git.bioconductor.org/packages/GSBenchMark
git_branch: RELEASE_3_21
git_last_commit: 38e89d8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSBenchMark_1.28.0.tar.gz
vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf
vignetteTitles: Working with the GSBenchMark package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R
suggestsMe: GSReg
dependencyCount: 0
Package: GSE103322
Version: 1.14.0
Depends: Biobase, GEOquery
Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
SummarizedExperiment, SingleCellExperiment
License: Artistic-2.0
MD5sum: 3665d48e383e05dc9f1b7406b6669349
NeedsCompilation: no
Title: GEO accession data GSE103322 as a SingleCellExperiment
Description: Single cell RNA-Seq data for 5902 cells from 18 patients
with oral cavity head and neck squamous cell carcinoma
available as GEO accession [GSE103322]
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322).
GSE103322 data have been parsed into a SincleCellExperiment
object available in ExperimentHub.
biocViews: ExperimentData, Genome, DNASeqData, RNASeqData,
ExperimentData, ExpressionData, RNASeqData, Homo_sapiens_Data,
CancerData, SingleCellData, GEO, ExperimentHub
Author: Mariano Alvarez [aut, cre]
Maintainer: Mariano Alvarez <reef103@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GSE103322
git_branch: RELEASE_3_21
git_last_commit: 9f32c39
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSE103322_1.14.0.tar.gz
vignettes: vignettes/GSE103322/inst/doc/GSE103322.html
vignetteTitles: scRNASeq HNSC data using Bioconductor's ExperimentHub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSE103322/inst/doc/GSE103322.R
dependencyCount: 77
Package: GSE13015
Version: 1.16.0
Depends: Biobase, GEOquery
Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase
Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown
License: MIT License
MD5sum: a0822d9e736e8417c02491643bfe2a24
NeedsCompilation: no
Title: GEO accession data GSE13015_GPL6106 as a SummarizedExperiment
Description: Microarray expression matrix platform GPL6106 and clinical
data for 67 septicemic patients and made them available as GEO
accession
[GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015).
GSE13015 data have been parsed into a SummarizedExperiment
object available in ExperimentHub. This data data could be used
as an example supporting BloodGen3Module R package.
biocViews: ExperimentData, MicroarrayData,ExperimentHub
Author: Darawan Rinchai [aut, cre] (ORCID:
<https://orcid.org/0000-0001-8851-7730>)
Maintainer: Darawan Rinchai <drinchai@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GSE13015
git_branch: RELEASE_3_21
git_last_commit: a888b4b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSE13015_1.16.0.tar.gz
vignettes: vignettes/GSE13015/inst/doc/GSE13015.html
vignetteTitles: Expression data from GSE13015 using Bioconductor's
ExperimentHub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GSE13015/inst/doc/GSE13015.R
dependencyCount: 78
Package: GSE159526
Version: 1.14.0
Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown,
testthat, minfi, tibble, sessioninfo
License: MIT + file LICENSE
MD5sum: b11d2907c2837c4e3028959de0e8597a
NeedsCompilation: no
Title: Placental cell DNA methylation data from GEO accession GSE159526
Description: 19 term and 9 first trimester placental chorionic villi
and matched cell-sorted samples ran on Illumina
HumanMethylationEPIC DNA methylation microarrays. This data was
made available on GEO accession
[GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526).
Both the raw and processed data has been made available on
\code{ExperimentHub}. Raw unprocessed data formatted as an
RGChannelSet object for integration and normalization using
minfi and other existing Bioconductor packages. Processed
normalized data is also available as a DNA methylation
\code{matrix}, with a corresponding phenotype information as a
\code{data.frame} object.
biocViews: ExperimentData, ExperimentHub, GEO, Genome, Tissue,
MethylationArrayData, Homo_sapiens_Data
Author: Victor Yuan [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3394-998X>)
Maintainer: Victor Yuan <victor.2wy@gmail.com>
URL: https://github.com/wvictor14/GSE159526
VignetteBuilder: knitr
BugReports: https://github.com/wvictor14/GSE159526/issues
git_url: https://git.bioconductor.org/packages/GSE159526
git_branch: RELEASE_3_21
git_last_commit: 2bd2a2a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSE159526_1.14.0.tar.gz
vignettes: vignettes/GSE159526/inst/doc/GSE159526.html
vignetteTitles: Introduction to GSE159526
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GSE159526/inst/doc/GSE159526.R
dependencyCount: 0
Package: GSE62944
Version: 1.36.0
Depends: Biobase, GEOquery
Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
DESeq2
License: Artistic-2.0
MD5sum: 004ec17d32e157795abca4e49df1e55e
NeedsCompilation: no
Title: GEO accession data GSE62944 as a SummarizedExperiment
Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal
samples across 24 cancer types and made them available as GEO
accession
[GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944).
GSE62944 data have been parsed into a SummarizedExperiment
object available in ExperimentHub.
biocViews: ExperimentData, Genome, DNASeqData, RNASeqData
Author: Sonali Arora
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GSE62944
git_branch: RELEASE_3_21
git_last_commit: 010e94e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSE62944_1.36.0.tar.gz
vignettes: vignettes/GSE62944/inst/doc/GSE62944.html
vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R
suggestsMe: GSEABenchmarkeR
dependencyCount: 77
Package: GSVAdata
Version: 1.44.0
Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db, SummarizedExperiment
License: Artistic-2.0
MD5sum: 21a084571c69520adb79b83b005768eb
NeedsCompilation: no
Title: Data employed in the vignette of the GSVA package
Description: This package stores the data employed in the vignette of
the GSVA package. These data belong to the following
publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy
et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature,
434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007;
Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al.
Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110,
2010; Costa et al. FEBS J, 288:2311-2331, 2021.
biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData,
LeukemiaCancerData
Author: Robert Castelo <robert.castelo@upf.edu>
Maintainer: Robert Castelo <robert.castelo@upf.edu>
git_url: https://git.bioconductor.org/packages/GSVAdata
git_branch: RELEASE_3_21
git_last_commit: 7cb2abf
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GSVAdata_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: singleCellTK, RVA
suggestsMe: GSAR, GSVA
dependencyCount: 63
Package: GWASdata
Version: 1.46.0
Depends: GWASTools
Suggests: ncdf4
License: Artistic-2.0
MD5sum: 6a2edb28b1ea404259e3b849ca631c06
NeedsCompilation: no
Title: Data used in the examples and vignettes of the GWASTools package
Description: Selected Affymetrix and Illlumina SNP data for HapMap
subjects. Data provided by the Center for Inherited Disease
Research at Johns Hopkins University and the Broad Institute of
MIT and Harvard University.
biocViews: ExperimentData, MicroarrayData, SNPData, HapMap
Author: Stephanie Gogarten
Maintainer: Stephanie Gogarten <sdmorris@uw.edu>
git_url: https://git.bioconductor.org/packages/GWASdata
git_branch: RELEASE_3_21
git_last_commit: 5088ff6
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/GWASdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GENESIS, GWASTools
dependencyCount: 96
Package: h5vcData
Version: 2.28.0
Suggests: h5vc
License: GPL (>= 3)
MD5sum: 49095d9918efb6dc5509bb7f60914519
NeedsCompilation: no
Title: Example data for the h5vc package
Description: This package contains the data used in the vignettes and
examples of the 'h5vc' package
biocViews: CancerData
Author: Paul Theodor Pyl
Maintainer: Paul Theodor Pyl <pyl@embl.de>
git_url: https://git.bioconductor.org/packages/h5vcData
git_branch: RELEASE_3_21
git_last_commit: 6b82461
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/h5vcData_2.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: h5vc
suggestsMe: HDF5Array
dependencyCount: 0
Package: hapmap100khind
Version: 1.50.0
Suggests: oligo
License: GPL
MD5sum: 9eee587d687b93dd4df3b4d7014e5988
NeedsCompilation: no
Title: Sample data - Hapmap 100K HIND Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, CancerData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap100khind
git_branch: RELEASE_3_21
git_last_commit: cf1ac79
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmap100khind_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmap100kxba
Version: 1.50.0
Suggests: oligo
License: GPL
MD5sum: 0011ea365d0a170a3cd595892868eebf
NeedsCompilation: no
Title: Sample data - Hapmap 100K XBA Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, CancerData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap100kxba
git_branch: RELEASE_3_21
git_last_commit: 5e54b85
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmap100kxba_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligo
dependencyCount: 0
Package: hapmap500knsp
Version: 1.50.0
Suggests: oligo
License: GPL
MD5sum: 01c20194dc9534a4a87e77375fb9c1d6
NeedsCompilation: no
Title: Sample data - Hapmap 500K NSP Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, CancerData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap500knsp
git_branch: RELEASE_3_21
git_last_commit: 4db326e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmap500knsp_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmap500ksty
Version: 1.50.0
Suggests: oligo
License: GPL
MD5sum: ebb5ccd9653d9b9d8c148914bc8bf65d
NeedsCompilation: no
Title: Sample data - Hapmap 500K STY Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, CancerData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap500ksty
git_branch: RELEASE_3_21
git_last_commit: d3b6505
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmap500ksty_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmapsnp5
Version: 1.50.0
Suggests: oligo
License: GPL
MD5sum: 8ecd888411c55c05f8d414bcae4d3f71
NeedsCompilation: no
Title: Sample data - Hapmap SNP 5.0 Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, CancerData, SNPData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmapsnp5
git_branch: RELEASE_3_21
git_last_commit: cdb91e3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmapsnp5_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligoClasses
dependencyCount: 0
Package: hapmapsnp6
Version: 1.50.0
Depends: R (>= 2.15)
Suggests: oligo, oligoClasses
License: GPL
MD5sum: 7786f393476772a2594bbc23305c984f
NeedsCompilation: no
Title: Sample data - Hapmap SNP 6.0 Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap, SNPData
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmapsnp6
git_branch: RELEASE_3_21
git_last_commit: 5aee0aa
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hapmapsnp6_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: crlmm, oligoClasses
dependencyCount: 0
Package: harbChIP
Version: 1.46.0
Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
Imports: methods, stats
License: Artistic-2.0
MD5sum: db02d295b080938b8957cbf4eb3d52cb
NeedsCompilation: no
Title: Experimental Data Package: harbChIP
Description: data from a yeast ChIP-chip experiment
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data,
SequencingData
Author: VJ Carey
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/harbChIP
git_branch: RELEASE_3_21
git_last_commit: 8aa02dc
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/harbChIP_1.46.0.tar.gz
vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf
vignetteTitles: upstream sequence management for yeast
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R
dependencyCount: 26
Package: HarmanData
Version: 1.36.0
Depends: R (>= 3.5.0)
Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3)
License: GPL-3
MD5sum: 5c8667ea0b7e29313b940538280a2cdc
NeedsCompilation: no
Title: Data for the Harman package
Description: Datasets of accompany Harman, a PCA and constrained
optimisation based technique. Contains three example datasets:
IMR90, Human lung fibroblast cells exposed to nitric oxide;
NPM, an experiment to test skin penetration of metal oxide
nanoparticles following topical application of sunscreens in
non-pregnant mice; OLF; an experiment to gauge the response of
human olfactory neurosphere-derived (hONS) cells to ZnO
nanoparticles. Since version 1.24, this package also contains
the Infinium5 dataset, a set of batch correction adjustments
across 5 Illumina Infinium Methylation BeadChip datasets. This
file does not contain methylation data, but summary statistics
of 5 datasets after correction. There is also an
EpiSCOPE_sample file as exampling for the new methylation
clustering functionality in Harman.
biocViews: ExpressionData, MicroarrayData, ExperimentData,
Homo_sapiens_Data, Mus_musculus_Data
Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre]
Maintainer: Jason Ross <jason.ross@csiro.au>
URL: http://www.bioinformatics.csiro.au/harman/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HarmanData
git_branch: RELEASE_3_21
git_last_commit: 8f2f2e9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HarmanData_1.36.0.tar.gz
vignettes: vignettes/HarmanData/inst/doc/HarmanData.html
vignetteTitles: HarmanData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HarmanData/inst/doc/HarmanData.R
suggestsMe: Harman
dependencyCount: 0
Package: HarmonizedTCGAData
Version: 1.30.0
Depends: R (>= 3.4.0)
Imports: ExperimentHub
Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
License: GPL-3
MD5sum: 068cb21247e9745c1b4d74504ff4f02d
NeedsCompilation: no
Title: Processed Harmonized TCGA Data of Five Selected Cancer Types
Description: This package contains the processed harmonized TCGA data
of five cancer types used in "Tianle Ma and Aidong Zhang,
Integrate Multi-omic Data Using Affinity Network Fusion (ANF)
for Cancer Patient Clustering".
biocViews: CancerData, ReproducibleResearch
Author: Tianle Ma
Maintainer: Tianle Ma <tianlema@buffalo.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData
git_branch: RELEASE_3_21
git_last_commit: 38e15e3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HarmonizedTCGAData_1.30.0.tar.gz
vignettes:
vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.html
vignetteTitles: Patient Affinity Matrices Derived from Harmonized TCGA
Dataset
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.R
dependencyCount: 65
Package: HCAData
Version: 1.24.0
Depends: R (>= 3.6), SingleCellExperiment
Imports: ExperimentHub, AnnotationHub, HDF5Array, utils
Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, scuttle, Rtsne, igraph, iSEE, testthat
License: MIT + file LICENSE
MD5sum: 3d9030589439d31990ce8c0af12152f9
NeedsCompilation: no
Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
Description: This package allows a direct access to the dataset
generated by the Human Cell Atlas project for further
processing in R and Bioconductor, in the comfortable format of
SingleCellExperiment objects (available in other formats here:
http://preview.data.humancellatlas.org/).
biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData,
ExperimentHub
Author: Federico Marini [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <marinif@uni-mainz.de>
URL: https://github.com/federicomarini/HCAData
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HCAData
git_branch: RELEASE_3_21
git_last_commit: 08c299a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HCAData_1.24.0.tar.gz
vignettes: vignettes/HCAData/inst/doc/hcadata.html
vignetteTitles: Accessing the Human Cell Atlas datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HCAData/inst/doc/hcadata.R
dependsOnMe: OSCA.workflows
dependencyCount: 82
Package: HCATonsilData
Version: 1.6.0
Depends: R (>= 4.3.0)
Imports: ExperimentHub, SingleCellExperiment, SpatialExperiment,
HDF5Array, SummarizedExperiment, S4Vectors, htmltools,
rmarkdown, base64enc, utils
Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac,
zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
License: MIT + file LICENSE
MD5sum: 10028472e488d8210bd6beb808a61018
NeedsCompilation: no
Title: Provide programmatic access to the tonsil cell atlas datasets
Description: This package provides access to the scRNA-seq, scATAC-seq,
multiome, CITE-seq and spatial transcriptomics (Visium) data
generated by the tonsil cell atlas in the context of the Human
Cell Atlas (HCA). The data is provided via the Bioconductor
project in the form of SingleCellExperiments. Additionally,
information on the whole compendium of identified cell types is
provided in form of a glossary.
biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub,
ExpressionData, SpatialData
Author: Ramon Massoni-Badosa [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7115-8145>), Federico Marini [aut]
(ORCID: <https://orcid.org/0000-0003-3252-7758>), Alan
O'Callaghan [aut], Helena L. Crowell [aut] (ORCID:
<https://orcid.org/0000-0002-4801-1767>)
Maintainer: Ramon Massoni-Badosa <ramonmassoni@gmail.com>
URL: https://github.com/massonix/HCATonsilData
VignetteBuilder: knitr
BugReports: https://github.com/massonix/HCATonsilData/issues
git_url: https://git.bioconductor.org/packages/HCATonsilData
git_branch: RELEASE_3_21
git_last_commit: a4e7b4b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HCATonsilData_1.6.0.tar.gz
vignettes: vignettes/HCATonsilData/inst/doc/HCATonsilData.html
vignetteTitles: HCATonsilData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HCATonsilData/inst/doc/HCATonsilData.R
dependencyCount: 100
Package: HD2013SGI
Version: 1.48.0
Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots,
limma, vcd, LSD,EBImage
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 022ca25ab31d24d73be0659eb77240c3
NeedsCompilation: no
Title: Mapping genetic interactions in human cancer cells with RNAi and
multiparametric phenotyping
Description: This package contains the experimental data and a complete
executable transcript (vignette) of the analysis of the HCT116
genetic interaction matrix presented in the paper "Mapping
genetic interactions in human cancer cells with RNAi and
multiparametric phenotyping" by C. Laufer, B. Fischer, M.
Billmann, W. Huber, M. Boutros; Nature Methods (2013)
10:427-31. doi: 10.1038/nmeth.2436.
biocViews: ExperimentData, CancerData, ColonCancerData,
MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data,
HighThroughputImagingData
Author: Bernd Fischer
Maintainer: Mike Smith <mike.smith@embl.de>
SystemRequirements: GNU make
git_url: https://git.bioconductor.org/packages/HD2013SGI
git_branch: RELEASE_3_21
git_last_commit: 3a8743c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HD2013SGI_1.48.0.tar.gz
vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf
vignetteTitles: HD2013SGI
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R
suggestsMe: splots
dependencyCount: 90
Package: HDCytoData
Version: 1.28.0
Depends: ExperimentHub, SummarizedExperiment, flowCore
Imports: utils, methods
Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust
License: MIT + file LICENSE
MD5sum: 8986ad86be6ae1d31900f8c03409d833
NeedsCompilation: no
Title: Collection of high-dimensional cytometry benchmark datasets in
Bioconductor object formats
Description: Data package containing a set of publicly available
high-dimensional cytometry benchmark datasets, formatted into
SummarizedExperiment and flowSet Bioconductor object formats,
including all required metadata. Row metadata includes sample
IDs, group IDs, patient IDs, reference cell population or
cluster labels (where available), and labels identifying
'spiked in' cells (where available). Column metadata includes
channel names, protein marker names, and protein marker classes
(cell type or cell state).
biocViews: ExperimentHub, ExperimentData, ExpressionData,
FlowCytometryData, SingleCellData, Homo_sapiens_Data,
ImmunoOncologyData
Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut]
Maintainer: Lukas M. Weber <lmweberedu@gmail.com>
URL: https://github.com/lmweber/HDCytoData
VignetteBuilder: knitr
BugReports: https://github.com/lmweber/HDCytoData/issues
git_url: https://git.bioconductor.org/packages/HDCytoData
git_branch: RELEASE_3_21
git_last_commit: 81e385d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HDCytoData_1.28.0.tar.gz
vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html,
vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html,
vignettes/HDCytoData/inst/doc/HDCytoData_package.html
vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases,
1. HDCytoData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R,
vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R,
vignettes/HDCytoData/inst/doc/HDCytoData_package.R
dependsOnMe: cytofWorkflow
suggestsMe: CytoMDS, diffcyt, tidyFlowCore, tidytof
dependencyCount: 82
Package: healthyControlsPresenceChecker
Version: 1.12.0
Depends: R (>= 4.0.0)
Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr
Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown
License: GPL-3
MD5sum: 3a9eb47b0da9b040ecaf3af1dc261588
NeedsCompilation: no
Title: Dowloads A Gene Expression Dataset From GEO And Checks If It
Contains Data Of Healthy Controls Or Not
Description: A function that reads in the GEO accession code of a gene
expression dataset, retrieves its data from GEO, and checks if
data of healthy controls are present in the dataset. It returns
true if healthy controls data are found, and false otherwise.
GEO: Gene Expression Omnibus. ID: identifier code. The GEO
datasets are downloaded from the URL
<https://ftp.ncbi.nlm.nih.gov/geo/series/>.
biocViews: GEO, RepositoryData, ExpressionData
Author: Davide Chicco [aut, cre] (ORCID:
<https://orcid.org/0000-0001-9655-7142>)
Maintainer: Davide Chicco <davide.chicco@gmail.com>
URL: https://github.com/davidechicco/healthyControlsPresenceChecker
VignetteBuilder: knitr
BugReports:
https://github.com/davidechicco/healthyControlsPresenceChecker/issues
git_url:
https://git.bioconductor.org/packages/healthyControlsPresenceChecker
git_branch: RELEASE_3_21
git_last_commit: 2d1173c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/healthyControlsPresenceChecker_1.12.0.tar.gz
vignettes:
vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.html
vignetteTitles: healthyControlsPresenceChecker vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.R
dependencyCount: 93
Package: healthyFlowData
Version: 1.46.0
Depends: R (>= 2.15.0), flowCore
Imports: methods
License: Artistic-2.0
MD5sum: 4c65caa33be97deb907f6d5961a507d0
NeedsCompilation: no
Title: Healthy dataset used by the flowMatch package
Description: A healthy dataset with 20 flow cytometry samples used by
the flowMatch package.
biocViews: FlowCytometryData
Author: Ariful Azad
Maintainer: Ariful Azad <aazad@purdue.edu>
git_url: https://git.bioconductor.org/packages/healthyFlowData
git_branch: RELEASE_3_21
git_last_commit: fb9c249
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/healthyFlowData_1.46.0.tar.gz
vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf
vignetteTitles: healthyFlowData: A healthy dataset with 20 flow
cytometry samples used by the flowMatch package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R
suggestsMe: flowMatch
dependencyCount: 18
Package: HEEBOdata
Version: 1.46.0
License: LGPL
MD5sum: eb375f8c0564cf8edeffe3a0037dbd05
NeedsCompilation: no
Title: HEEBO set and HEEBO controls.
Description: R objects describing the HEEBO oligo set.
biocViews: ExperimentData
Author: Agnes Paquet
Maintainer: Agnes Paquet <apaquet@medsfgh.ucsf.edu>
URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/
git_url: https://git.bioconductor.org/packages/HEEBOdata
git_branch: RELEASE_3_21
git_last_commit: 66e2155
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HEEBOdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQuality
dependencyCount: 0
Package: HelloRangesData
Version: 1.34.0
Suggests: BiocStyle
License: GPL (>= 2)
MD5sum: 9d6a6dc974ec138e73b237b07406d121
NeedsCompilation: no
Title: Data for the HelloRanges tutorial vignette
Description: Provides the data that were used in the bedtools tutorial
by Aaron Quinlan
(http://quinlanlab.org/tutorials/bedtools/bedtools.html).
Includes a subset of the DnaseI hypersensitivity data from
"Maurano et al. Systematic Localization of Common
Disease-Associated Variation in Regulatory DNA. Science. 2012.
Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were
originally downloaded from the UCSC table browser. See the
HelloRanges vignette for a port of the bedtools tutorial to R.
biocViews: ExperimentData, SequencingData
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
git_url: https://git.bioconductor.org/packages/HelloRangesData
git_branch: RELEASE_3_21
git_last_commit: 82ffbcd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HelloRangesData_1.34.0.tar.gz
vignettes: vignettes/HelloRangesData/inst/doc/intro.pdf
vignetteTitles: HelloRanges Example Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HelloRangesData/inst/doc/intro.R
suggestsMe: HelloRanges, plyranges
dependencyCount: 0
Package: hgu133abarcodevecs
Version: 1.46.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 9e727def5d3b414d386573ad171523f2
NeedsCompilation: no
Title: hgu133a data for barcode
Description: Data used by the barcode package for microarrays of type
hgu133a.
biocViews: Homo_sapiens_Data, MicroarrayData
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs
git_branch: RELEASE_3_21
git_last_commit: d52f041
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hgu133abarcodevecs_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hgu133plus2barcodevecs
Version: 1.46.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 02dc8d1b6515719ba6a57b539bf10af3
NeedsCompilation: no
Title: hgu133plus2 data for barcode
Description: Data used by the barcode package for microarrays of type
hgu133plus2.
biocViews: Homo_sapiens_Data, MicroarrayData
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs
git_branch: RELEASE_3_21
git_last_commit: 649f8f5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hgu133plus2barcodevecs_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hgu133plus2CellScore
Version: 1.28.0
Depends: R (>= 3.5.0)
Imports: Biobase (>= 2.39.1)
Suggests: knitr
License: GPL-3
MD5sum: 5092860dcd17e6c19e2931f215326ff0
NeedsCompilation: no
Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2]
Description: The CellScore Standard Dataset contains expression data
from a wide variety of human cells and tissues, which should be
used as standard cell types in the calculation of the
CellScore. All data was curated from public databases such as
Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or
ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This
standard dataset only contains data from the Affymetrix
GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were
manually annotated using the database information or consulting
the publications in which the datasets originated. The sample
annotations are stored in the phenoData slot of the
expressionSet object. Raw data (CEL files) were processed with
the affy package to generate present/absent calls (mas5calls)
and background-subtracted values, which were then normalized by
the R-package yugene to yield the final expression values for
the standard expression matrix. The annotation table for the
microarray was retrieved from the BioC annotation package
hgu133plus2. All data are stored in an expressionSet object.
biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData,
Homo_sapiens_Data, Genome, ArrayExpress
Author: Nancy Mah, Katerina Taskova
Maintainer: Nancy Mah <nancy.l.mah@googlemail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore
git_branch: RELEASE_3_21
git_last_commit: e841026
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hgu133plus2CellScore_1.28.0.tar.gz
vignettes:
vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf
vignetteTitles: R packages: hgu133plus2CellScore
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R
suggestsMe: CellScore
dependencyCount: 7
Package: hgu2beta7
Version: 1.48.0
Depends: R (>= 2.0.0)
License: Artistic-2.0
MD5sum: 40461ab83f457e5caddd8080c185c74d
NeedsCompilation: no
Title: A data package containing annotation data for hgu2beta7
Description: Annotation data file for hgu2beta7 assembled using data
from public data repositories
biocViews: Genome
Author: Chenwei Lin
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
git_url: https://git.bioconductor.org/packages/hgu2beta7
git_branch: RELEASE_3_21
git_last_commit: 7525d24
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/hgu2beta7_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: HiBED
Version: 1.6.0
Depends: R (>= 3.5.0)
Imports: dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k,
minfi, utils, AnnotationHub, SummarizedExperiment
Suggests: knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest
License: GPL-3
MD5sum: 0a0b2fcb05df23e9cd699b778b2730d7
NeedsCompilation: no
Title: HiBED
Description: Hierarchical deconvolution for extensive cell type
resolution in the human brain using DNA methylation. The HiBED
deconvolution estimates proportions up to 7 cell types
(GABAergic neurons, glutamatergic neurons, astrocytes,
microglial cells, oligodendrocytes, endothelial cells, and
stromal cells) in bulk brain tissues.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
Genome, MethylationArrayData, PackageTypeData
Author: Ze Zhang [cre, aut] (ORCID:
<https://orcid.org/0000-0001-9854-5823>), Lucas A. Salas [aut]
Maintainer: Ze Zhang <ze.zhang.gr@dartmouth.edu>
URL: https://github.com/SalasLab/HiBED
VignetteBuilder: knitr
BugReports: https://github.com/SalasLab/HiBED/issues.
git_url: https://git.bioconductor.org/packages/HiBED
git_branch: RELEASE_3_21
git_last_commit: f53309b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HiBED_1.6.0.tar.gz
vignettes: vignettes/HiBED/inst/doc/HiBED.html
vignetteTitles: HiBED
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HiBED/inst/doc/HiBED.R
dependencyCount: 153
Package: HiCDataHumanIMR90
Version: 1.28.0
Depends: R (>= 3.5.0)
Suggests: HiTC, BiocStyle
License: GPL-3
MD5sum: 9f84794c68a444a744695671bc2a31cd
NeedsCompilation: no
Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012
Description: The HiC data from Human Fibroblast IMR90 cell line
(HindIII restriction) was retrieved from the GEO website,
accession number GSE35156
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156).
The raw reads were processed as explained in Dixon et al.
(Nature 2012).
biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO
Author: Nicolas Servant
Maintainer: Nicolas Servant <Nicolas.Servant@curie.fr>
git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90
git_branch: RELEASE_3_21
git_last_commit: ffeee9e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HiCDataHumanIMR90_1.28.0.tar.gz
vignettes: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.pdf
vignetteTitles: HiC Data Human Fibroblast Dixon et al. 2012
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.R
suggestsMe: HiTC
dependencyCount: 0
Package: HiCDataLymphoblast
Version: 1.44.0
Suggests: ShortRead
License: GPL-3
MD5sum: cc6045d5e939b83b0740d2a59db0c5e5
NeedsCompilation: no
Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009
Description: The HiC data from human lymphoblastoid cell line (HindIII
restriction) was retrieved from the sequence read archive and
two ends of the paired reads were aligned separately with
bowtie.
biocViews: ExperimentData, Homo_sapiens_Data
Author: Borbala Mifsud
Maintainer: Borbala Mifsud <b.mifsud@qmul.ac.uk>
git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast
git_branch: RELEASE_3_21
git_last_commit: 76b1851
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HiCDataLymphoblast_1.44.0.tar.gz
vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf
vignetteTitles: package_vignettes.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R
suggestsMe: GOTHiC
dependencyCount: 0
Package: HiContactsData
Version: 1.10.0
Depends: ExperimentHub
Imports: BiocFileCache, AnnotationHub
Suggests: testthat, methods, BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 3e72118c67f34f87d96628505e1505b5
NeedsCompilation: no
Title: HiContacts companion data package
Description: Provides a collection of Hi-C files (pairs, (m)cool and
fastq). These datasets can be read into R and further
investigated and visualized with the HiContacts package. Data
includes yeast Hi-C data generated by the Koszul lab from the
Pasteur Institute.
biocViews: ExperimentHub, ExperimentData, SequencingData
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
URL: https://github.com/js2264/HiContactsData
VignetteBuilder: knitr
BugReports: https://github.com/js2264/HiContactsData/issues
git_url: https://git.bioconductor.org/packages/HiContactsData
git_branch: RELEASE_3_21
git_last_commit: ff43824
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HiContactsData_1.10.0.tar.gz
vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html
vignetteTitles: HiContactsData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R
importsMe: OHCA
suggestsMe: HiCExperiment, HiContacts, HiCool, plyinteractions
dependencyCount: 65
Package: HighlyReplicatedRNASeq
Version: 1.20.0
Depends: SummarizedExperiment, ExperimentHub
Imports: S4Vectors
Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 0dddc58aedb401596502dd3b02d5606e
NeedsCompilation: no
Title: Collection of Bulk RNA-Seq Experiments With Many Replicates
Description: Gene-level count matrix data for bulk RNA-seq dataset with
many replicates. The data are provided as easy to use
SummarizedExperiment objects. The source data that is made
accessible through this package comes from
https://github.com/bartongroup/profDGE48.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData
Author: Constantin Ahlmann-Eltze [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3762-068X>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
URL: https://github.com/const-ae/HighlyReplicatedRNASeq
VignetteBuilder: knitr
BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues
git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq
git_branch: RELEASE_3_21
git_last_commit: 03054fc
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HighlyReplicatedRNASeq_1.20.0.tar.gz
vignettes:
vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.html
vignetteTitles: Exploring the 86 bulk RNA-seq samples from the Schurch
et al. (2016) study
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles:
vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.R
dependencyCount: 76
Package: Hiiragi2013
Version: 1.44.2
Depends: R (>= 4.0.0), KEGGREST, affy, boot, clue, genefilter,
geneplotter, gtools, mouse4302.db, xtable
Imports: MASS, Biobase, RColorBrewer, cluster, gplots, grid, lattice,
latticeExtra
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 70afb678b36c343c88b4995026f9fe3f
NeedsCompilation: no
Title: Cell-to-cell expression variability followed by signal
reinforcement progressively segregates early mouse lineages
Description: This package contains the experimental data and a complete
executable transcript (vignette) of the statistical analysis
presented in the paper "Cell-to-cell expression variability
followed by signal reinforcement progressively segregates early
mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang,
P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M.
Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology
(2014) 16(1): 27-37. doi: 10.1038/ncb2881."
biocViews: ExperimentData, MicroarrayData, qPCRData,
ReproducibleResearch
Author: Andrzej Oles, Wolfgang Huber
Maintainer: Wolfgang Huber <wolfgang.huber@embl.org>
git_url: https://git.bioconductor.org/packages/Hiiragi2013
git_branch: RELEASE_3_21
git_last_commit: 28c44d1
git_last_commit_date: 2025-05-27
Date/Publication: 2025-06-05
source.ver: src/contrib/Hiiragi2013_1.44.2.tar.gz
vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf
vignetteTitles: Hiiragi2013
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R
dependencyCount: 79
Package: HIVcDNAvantWout03
Version: 1.48.0
License: GPL (>= 2)
MD5sum: ea4b70cc323914c8e13b21796902a587
NeedsCompilation: no
Title: T cell line infections with HIV-1 LAI (BRU)
Description: The expression levels of approximately 4600 cellular RNA
transcripts were assessed in CD4+ T cell lines at different
times after infection with HIV-1BRU using DNA microarrays. This
data corresponds to the first block of a 12 block array image
(001030_08_1.GEL) in the first data set (2000095918 A) in the
first experiment (CEM LAI vs HI-LAI 24hr). There are two data
sets, which are part of a dye-swap experiment with replicates,
representing the Cy3 (green) absorption intensities for channel
1 (hiv1raw) and the Cy5 (red) absorption intensities for
channel 2 (hiv2raw).
biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData
Author: Dr. Angelique van't Wout, Department of Microbiology,
University of Washington
Maintainer: Chris Fraley <fraley@stat.washington.edu>
URL:
http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html
git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03
git_branch: RELEASE_3_21
git_last_commit: d317f0a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HIVcDNAvantWout03_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: HMP16SData
Version: 1.28.0
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr,
kableExtra, knitr, magrittr, methods, readr, stringr, tibble,
utils
Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize,
cowplot, dendextend, devtools, ggplot2, gridExtra, haven,
phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
License: Artistic-2.0
MD5sum: a8ac06413d827310f99c46b2550eef86
NeedsCompilation: no
Title: 16S rRNA Sequencing Data from the Human Microbiome Project
Description: HMP16SData is a Bioconductor ExperimentData package of the
Human Microbiome Project (HMP) 16S rRNA sequencing data for
variable regions 1–3 and 3–5. Raw data files are provided in
the package as downloaded from the HMP Data Analysis and
Coordination Center. Processed data is provided as
SummarizedExperiment class objects via ExperimentHub.
biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data,
MicrobiomeData, ReproducibleResearch, SequencingData
Author: Lucas schiffer [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3628-0326>), Rimsha Azhar [aut],
Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron
[aut]
Maintainer: Lucas schiffer <schiffer.lucas@gmail.com>
URL: https://github.com/waldronlab/HMP16SData
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/HMP16SData/issues
git_url: https://git.bioconductor.org/packages/HMP16SData
git_branch: RELEASE_3_21
git_last_commit: a58e99b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HMP16SData_1.28.0.tar.gz
vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html
vignetteTitles: HMP16SData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R
dependencyCount: 109
Package: HMP2Data
Version: 1.22.0
Depends: R (>= 3.6.0)
Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors,
SummarizedExperiment, phyloseq, MultiAssayExperiment,
data.table
Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot,
devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2,
stats, testthat, tibble, UpSetR
License: Artistic-2.0
MD5sum: 6ebbe9ebcb9df38b4e27e5a5e2fc54d2
NeedsCompilation: no
Title: 16s rRNA sequencing data from the Human Microbiome Project 2
Description: HMP2Data is a Bioconductor package of the Human Microbiome
Project 2 (HMP2) 16S rRNA sequencing data. Processed data is
provided as phyloseq, SummarizedExperiment, and
MultiAssayExperiment class objects. Individual matrices and
data.frames used for building these S4 class objects are also
provided in the package.
biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData,
ReproducibleResearch, SequencingData
Author: John Stansfield <stansfieldjc@vcu.edu>, Ekaterina Smirnova
<ekaterina.smirnova@vcuhealth.org>, Ni Zhao <nzhao10@jhu.edu>,
Jennifer Fettweis <jennifer.fettweis@vcuhealth.org>, Levi
Waldron <levi.waldron@sph.cuny.edu>, Mikhail Dozmorov
<mikhail.dozmorov@vcuhealth.org>
Maintainer: John Stansfield <stansfieldjc@vcu.edu>, Ekaterina Smirnova
<ekaterina.smirnova@vcuhealth.org>
URL: https://github.com/jstansfield0/HMP2Data
VignetteBuilder: knitr
BugReports: https://github.com/jstansfield0/HMP2Data/issues
git_url: https://git.bioconductor.org/packages/HMP2Data
git_branch: RELEASE_3_21
git_last_commit: f0685e3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HMP2Data_1.22.0.tar.gz
vignettes: vignettes/HMP2Data/inst/doc/hmp2data.html
vignetteTitles: HMP2Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HMP2Data/inst/doc/hmp2data.R
dependencyCount: 142
Package: homosapienDEE2CellScore
Version: 1.4.0
Imports: Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics,
DESeq2, S4Vectors, SummarizedExperiment, getDEE2,
MatrixGenerics
Suggests: knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager,
AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore
(>= 1.21.4)
License: GPL (>= 3)
MD5sum: b64d70f7bc413413df254d5dd534b049
NeedsCompilation: no
Title: Example Data Package for CellScore
Description: This is a data package for normalised homosapien data
downloaded from DEE2. The package both downloads, normalises,
and filters the data, and provides a way to access the data
from a canonical store without needing local processing. This
package was built as a way to generate and store canonical test
data for CellScore.
biocViews: RNASeqData, Genome, ExperimentHub, ExpressionData
Author: Justin Marsh [aut, cre]
Maintainer: Justin Marsh <j.marsh@auckland.ac.nz>
VignetteBuilder: knitr
BugReports: https://github.com/flaviusb/homosapienDEE2CellScore/issues
git_url: https://git.bioconductor.org/packages/homosapienDEE2CellScore
git_branch: RELEASE_3_21
git_last_commit: 19b56b0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/homosapienDEE2CellScore_1.4.0.tar.gz
vignettes:
vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.html
vignetteTitles: Use the Data in this Data Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.R
dependencyCount: 104
Package: HSMMSingleCell
Version: 1.28.0
Depends: R (>= 2.10)
License: Artistic-2.0
MD5sum: 3deb4aa5d79124c165d0ad7e70855864
NeedsCompilation: no
Title: Single-cell RNA-Seq for differentiating human skeletal muscle
myoblasts (HSMM)
Description: Skeletal myoblasts undergo a well-characterized sequence
of morphological and transcriptional changes during
differentiation. In this experiment, primary human skeletal
muscle myoblasts (HSMM) were expanded under high mitogen
conditions (GM) and then differentiated by switching to
low-mitogen media (DM). RNA-Seq libraries were sequenced from
each of several hundred cells taken over a time-course of
serum-induced differentiation. Between 49 and 77 cells were
captured at each of four time points (0, 24, 48, 72 hours)
following serum switch using the Fluidigm C1 microfluidic
system. RNA from each cell was isolated and used to construct
mRNA-Seq libraries, which were then sequenced to a depth of ~4
million reads per library, resulting in a complete gene
expression profile for each cell.
biocViews: ExperimentData, RNASeqData
Author: Cole Trapnell
Maintainer: Cole Trapnell <cole@broadinstitute.org>
git_url: https://git.bioconductor.org/packages/HSMMSingleCell
git_branch: RELEASE_3_21
git_last_commit: cdf07e9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HSMMSingleCell_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: monocle
dependencyCount: 0
Package: HumanAffyData
Version: 1.34.0
Depends: ExperimentHub, Biobase, R (>= 3.3)
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 8b2c4d24c6a53cbb8446899c78714ae2
NeedsCompilation: no
Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as
ExpressionSet objects
Description: Re-analysis of human gene expression data generated on the
Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A
(EH177) platforms. The original data were normalized using
robust multiarray averaging (RMA) to obtain an integrated gene
expression atlas across diverse biological sample types and
conditions. The entire compendia comprisee 9395 arrays for
EH176 and 5372 arrays for EH177.
biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data,
MicroarrayData, ExpressionData
Author: Brad Nelms
Maintainer: Brad Nelms <bnelms.research@gmail.com>
git_url: https://git.bioconductor.org/packages/HumanAffyData
git_branch: RELEASE_3_21
git_last_commit: 43d98e1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/HumanAffyData_1.34.0.tar.gz
vignettes: vignettes/HumanAffyData/inst/doc/HumanAffyData.pdf
vignetteTitles: Intro to the HumanAffyData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HumanAffyData/inst/doc/HumanAffyData.R
suggestsMe: CellMapper
dependencyCount: 65
Package: humanHippocampus2024
Version: 1.0.0
Depends: R (>= 4.4)
Imports: ExperimentHub, SummarizedExperiment,SpatialExperiment
Suggests: testthat (>= 3.0.0), sessioninfo, rmarkdown, knitr,
BiocStyle, ExperimentHubData, AnnotationHubData, RefManageR
License: Artistic-2.0
MD5sum: 63ab626cd811134da4d218afbc2f704a
NeedsCompilation: no
Title: Access to SRT and snRNA-seq data from spatial_HPC project
Description: This is an ExperimentHub Data package that helps to access
the spatially-resolved transcriptomics and single-nucleus RNA
sequencing data. The datasets are generated from adjacent
tissue sections of the anterior human hippocampus across ten
adult neurotypical donors. The datasets are based on
[spatial_hpc](https://github.com/LieberInstitute/spatial_hpc)
project by Lieber Institute for Brain Development (LIBD)
researchers and collaborators.
biocViews: ExperimentHub, SequencingData, SpatialData, ExpressionData,
Tissue, RNASeqData
Author: Christine Hou [aut, cre] (ORCID:
<https://orcid.org/0009-0001-5350-0629>)
Maintainer: Christine Hou <chris2018hou@gmail.com>
URL: https://github.com/LieberInstitute/spatial_hpc,
https://christinehou11.github.io/humanHippocampus2024/
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/humanHippocampus2024
git_url: https://git.bioconductor.org/packages/humanHippocampus2024
git_branch: RELEASE_3_21
git_last_commit: 39f0a1c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/humanHippocampus2024_1.0.0.tar.gz
vignettes:
vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.html
vignetteTitles: humanHippocampus2024 Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.R
dependencyCount: 81
Package: humanStemCell
Version: 0.48.0
Depends: Biobase (>= 2.5.5), hgu133plus2.db
License: Artistic-2.0
MD5sum: 1aab77c21b6777038955dd4b602c6463
NeedsCompilation: no
Title: Human Stem Cells time course experiment
Description: Affymetrix time course experiment on human stem cells (two
time points: undifferentiated and differentiated).
biocViews: ExperimentData, Homo_sapiens_Data
Author: R. Gentleman, N. Le Meur, M. Tewari
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/humanStemCell
git_branch: RELEASE_3_21
git_last_commit: 8f4dead
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/humanStemCell_0.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MiRaGE, rtracklayer
dependencyCount: 47
Package: IHWpaper
Version: 1.36.0
Depends: R (>= 3.3), IHW
Imports: Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
LinkingTo: Rcpp
Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
License: Artistic-2.0
MD5sum: 856e07ecc203f5276d4ac74a15a8d02f
NeedsCompilation: yes
Title: Reproduce figures in IHW paper
Description: This package conveniently wraps all functions needed to
reproduce the figures in the IHW paper
(https://www.nature.com/articles/nmeth.3885) and the data
analysis in
https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf.
the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it
is a companion package to the Bioconductor IHW package.
biocViews: ReproducibleResearch, ExperimentData, RNASeqData,
ExpressionData
Author: Nikos Ignatiadis [aut, cre]
Maintainer: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/IHWpaper
git_branch: RELEASE_3_21
git_last_commit: 5a3820c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/IHWpaper_1.36.0.tar.gz
vignettes: vignettes/IHWpaper/inst/doc/BH-explanation.html,
vignettes/IHWpaper/inst/doc/explaining_tdr.html,
vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.html,
vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.html,
vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.html,
vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.html,
vignettes/IHWpaper/inst/doc/real_data_examples.html,
vignettes/IHWpaper/inst/doc/simulations_vignette.html,
vignettes/IHWpaper/inst/doc/stratified_histograms.html,
vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.html,
vignettes/IHWpaper/inst/doc/weights_vs_filtering.html
vignetteTitles: "Various: BH explanation / visualization", "NMeth
paper: Explaining tdr", "Various: Grenander Estimator as
applied to IHW (vs ECDF)", "Stats paper: hQTL analysis with
IHW-Benjamini-Yekutieli", "NMeth paper: IHW-Bonferroni
simulations", "Various: Real data examples: 1-fold weight
function", "NMeth paper: Real data examples", "NMeth paper:
Simulation Figures", "NMeth paper: Stratified Histograms",
"Various: tdr and pvalue rejection regions", "Various: Weights
vs Independent Filtering"
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IHWpaper/inst/doc/BH-explanation.R,
vignettes/IHWpaper/inst/doc/explaining_tdr.R,
vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.R,
vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.R,
vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.R,
vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.R,
vignettes/IHWpaper/inst/doc/real_data_examples.R,
vignettes/IHWpaper/inst/doc/simulations_vignette.R,
vignettes/IHWpaper/inst/doc/stratified_histograms.R,
vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.R,
vignettes/IHWpaper/inst/doc/weights_vs_filtering.R
dependencyCount: 103
Package: Illumina450ProbeVariants.db
Version: 1.44.0
Depends: R (>= 3.0.1)
License: GPL-3
MD5sum: eaaafd5ddbf1d234c7f029c6b970133e
NeedsCompilation: no
Title: Annotation Package combining variant data from 1000 Genomes
Project for Illumina HumanMethylation450 Bead Chip probes
Description: Includes details on variants for each probe on the 450k
bead chip for each of the four populations (Asian, American,
African and European)
biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData
Author: Lee Butcher
Maintainer: Tiffany Morris <tiffany.morris@ucl.ac.uk>
git_url:
https://git.bioconductor.org/packages/Illumina450ProbeVariants.db
git_branch: RELEASE_3_21
git_last_commit: 569a40c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Illumina450ProbeVariants.db_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: IlluminaDataTestFiles
Version: 1.46.0
License: Artistic-2.0
MD5sum: 00f11739bd4d1720f1cdada3baa84671
NeedsCompilation: no
Title: Illumina microarray files (IDAT) for testing
Description: Example data for Illumina microarray output files, for
testing purposes
biocViews: MicroarrayData
Author: Kasper Daniel Hansen, Mike L. Smith
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles
git_branch: RELEASE_3_21
git_last_commit: 6658404
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/IlluminaDataTestFiles_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: illuminaio
dependencyCount: 0
Package: imcdatasets
Version: 1.16.0
Depends: R (>= 4.4.0), SingleCellExperiment, SpatialExperiment,
cytomapper,
Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray,
HDF5Array
Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat
License: GPL-3 + file LICENSE
MD5sum: 1d2b44d60dc8b3456f1f11271c597a4d
NeedsCompilation: no
Title: Collection of publicly available imaging mass cytometry (IMC)
datasets
Description: The imcdatasets package provides access to publicly
available IMC datasets. IMC is a technology that enables
measurement of > 40 proteins from tissue sections. The
generated images can be segmented to extract single cell data.
Datasets typically consist of three elements: a
SingleCellExperiment object containing single cell data, a
CytoImageList object containing multichannel images and a
CytoImageList object containing the cell masks that were used
to extract the single cell data from the images.
biocViews: ExperimentData, ExperimentHub, SingleCellData, SpatialData,
Homo_sapiens_Data, ImmunoOncologyData, TechnologyData,
PackageTypeData, ReproducibleResearch, Tissue
Author: Nicolas Damond [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3027-8989>), Nils Eling [ctb]
(ORCID: <https://orcid.org/0000-0002-4711-1176>), Fischer Jana
[ctb] (ORCID: <https://orcid.org/0000-0001-9047-8400>)
Maintainer: Nicolas Damond <nicolas.damond@dqbm.uzh.ch>
URL: https://github.com/BodenmillerGroup/imcdatasets
VignetteBuilder: knitr
BugReports: https://github.com/BodenmillerGroup/imcdatasets/issues
git_url: https://git.bioconductor.org/packages/imcdatasets
git_branch: RELEASE_3_21
git_last_commit: 829ab88
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/imcdatasets_1.16.0.tar.gz
vignettes:
vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.html,
vignettes/imcdatasets/inst/doc/imcdatasets.html
vignetteTitles: "Contributing guidelines and datasets format",
"Accessing IMC datasets"
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles:
vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.R,
vignettes/imcdatasets/inst/doc/imcdatasets.R
dependencyCount: 151
Package: ITALICSData
Version: 2.46.0
Depends: R (>= 2.0.0)
License: GPL
MD5sum: bd7ec53b1fbbfaf1ad177c1741fbcebb
NeedsCompilation: no
Title: ITALICSData
Description: Data needed to use the ITALICS package
biocViews: ExperimentData, HapMap
Author: Guillem Rigaill
Maintainer: Guillem Rigaill <italics@curie.fr>
URL: http://bioinfo.curie.fr
git_url: https://git.bioconductor.org/packages/ITALICSData
git_branch: RELEASE_3_21
git_last_commit: c440a82
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ITALICSData_2.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ITALICS
dependencyCount: 0
Package: Iyer517
Version: 1.50.0
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: d17d396bc2b579c83357ff8bd677f2b1
NeedsCompilation: no
Title: exprSets for Iyer, Eisen et all 1999 Science paper
Description: representation of public Iyer data from
http://genome-www.stanford.edu/serum/clusters.html
biocViews: ExperimentData
Author: Vishy Iyer <vishy@cmgm.stanford.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/Iyer517
git_branch: RELEASE_3_21
git_last_commit: 86347bb
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Iyer517_1.50.0.tar.gz
vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf
vignetteTitles: Iyer517
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R
dependencyCount: 7
Package: JASPAR2014
Version: 1.44.0
Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19)
License: GPL-2
MD5sum: 5be61f02a3cbd63a6f3a113247d7f630
NeedsCompilation: no
Title: Data package for JASPAR
Description: Data package for JASPAR 2014. To search this databases,
please use the package TFBSTools.
biocViews: ExperimentData, SequencingData
Author: Ge Tan <ge_tan@live.com>
Maintainer: Ge Tan <ge_tan@live.com>
URL: http://jaspar.genereg.net/
git_url: https://git.bioconductor.org/packages/JASPAR2014
git_branch: RELEASE_3_21
git_last_commit: 2b44661
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/JASPAR2014_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MatrixRider, TFBSTools
dependencyCount: 25
Package: JASPAR2016
Version: 1.36.0
Depends: R (>= 3.2.2), methods
License: GPL-2
MD5sum: 88a0ec591686c681719a9a4c62d1a18e
NeedsCompilation: no
Title: Data package for JASPAR 2016
Description: Data package for JASPAR 2016. To search this databases,
please use the package TFBSTools (>= 1.8.1).
biocViews: ExperimentData, MotifAnnotation, GeneRegulation
Author: Ge Tan <ge_tan@live.com>
Maintainer: Ge Tan <ge_tan@live.com>
URL: http://jaspar.genereg.net/
git_url: https://git.bioconductor.org/packages/JASPAR2016
git_branch: RELEASE_3_21
git_last_commit: 50f37b9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/JASPAR2016_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: chromVAR, TFBSTools, CAGEWorkflow
dependencyCount: 1
Package: JohnsonKinaseData
Version: 1.4.0
Depends: R (>= 4.1.0)
Imports: ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr,
tidyr, purrr, utils
Suggests: knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0),
rmarkdown
License: MIT + file LICENSE
MD5sum: 9be69b1a7948c14f6c3685dec59a06fb
NeedsCompilation: no
Title: Kinase PWMs based on data published by Johnson et al. 2023 and
Yaron-Barir et al. 2024
Description: The packages provides position specific weight matrices
(PWMs) for 303 human serine/threonine and 93 tyrosine kinases
originally published in Johnson et al. 2023
(doi:10.1038/s41586-022-05575-3) and Yaron-Barir et al. 2024
(doi:10.1038/s41586-024-07407-y). The package includes basic
functionality to score user provided phosphosites. It also
includes pre-computed PWM scores ("background scores") for a
large collection of curated human phosphosites which can be
used to rank PWM scores relative to the background scores
("percentile rank").
biocViews: ExperimentHub, Homo_sapiens_Data, Proteome
Author: Florian Geier [aut, cre] (ORCID:
<https://orcid.org/0000-0002-9076-9264>)
Maintainer: Florian Geier <florian.geier@unibas.ch>
URL: https://github.com/fgeier/JohnsonKinaseData/
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/JohnsonKinaseData
git_url: https://git.bioconductor.org/packages/JohnsonKinaseData
git_branch: RELEASE_3_21
git_last_commit: 1073ddd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/JohnsonKinaseData_1.4.0.tar.gz
vignettes: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.html
vignetteTitles: JohnsonKinaseData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.R
dependencyCount: 76
Package: KEGGandMetacoreDzPathwaysGEO
Version: 1.28.0
Depends: R (>= 2.15.0)
Imports: Biobase, BiocGenerics
License: GPL-2
MD5sum: 1ae6a75a7c982b3739a890c70255aa28
NeedsCompilation: no
Title: Disease Datasets from GEO
Description: This is a collection of 18 data sets for which the
phenotype is a disease with a corresponding pathway in either
KEGG or metacore database.This collection of datasets were used
as gold standard in comparing gene set analysis methods.
biocViews: ExperimentData, GEO
Author: Gaurav Bhatti
Maintainer: Gaurav Bhatti <gbhatti@med.wayne.edu>
git_url:
https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO
git_branch: RELEASE_3_21
git_last_commit: fb4d093
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.28.0.tar.gz
vignettes:
vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf
vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R
importsMe: GSEABenchmarkeR
dependencyCount: 7
Package: KEGGdzPathwaysGEO
Version: 1.46.0
Depends: R (>= 2.13.0)
Imports: Biobase, BiocGenerics
License: GPL-2
MD5sum: fcc71c5b1d8b76427c4e52967c6b4aa7
NeedsCompilation: no
Title: KEGG Disease Datasets from GEO
Description: This is a collection of 24 data sets for which the
phenotype is a disease with a corresponding pathway in the KEGG
database.This collection of datasets were used as gold standard
in comparing gene set analysis methods by the PADOG package.
biocViews: MicroarrayData, GEO, ExperimentData
Author: Gaurav Bhatti, Adi L. Tarca
Maintainer: Gaurav Bhatti <gbhatti@med.wayne.edu>
git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
git_branch: RELEASE_3_21
git_last_commit: 3b4f21a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/KEGGdzPathwaysGEO_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: PADOG
importsMe: GSEABenchmarkeR
dependencyCount: 7
Package: kidpack
Version: 1.50.0
Depends: R (>= 2.6.0), Biobase (>= 2.5.5)
License: GPL-2
MD5sum: e42c86932bd54cf069390fbfbc43d035
NeedsCompilation: no
Title: DKFZ kidney package
Description: kidney microarray data
biocViews: ExperimentData, CancerData, KidneyCancerData,
MicroarrayData, ArrayExpress
Author: Wolfgang Huber <huber@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.dkfz.de/mga
git_url: https://git.bioconductor.org/packages/kidpack
git_branch: RELEASE_3_21
git_last_commit: ebde15c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/kidpack_1.50.0.tar.gz
vignettes: vignettes/kidpack/inst/doc/kidpack.pdf
vignetteTitles: kidpack - overview over the DKFZ kidney data package
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/kidpack/inst/doc/kidpack.R
dependencyCount: 7
Package: KOdata
Version: 1.34.0
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
MD5sum: 26cd461cc628ade643b0c28ab2362d85
NeedsCompilation: no
Title: LINCS Knock-Out Data Package
Description: Contains consensus genomic signatures (CGS) for
experimental cell-line specific gene knock-outs as well as
baseline gene expression data for a subset of experimental
cell-lines. Intended for use with package KEGGlincs.
biocViews: ExpressionData, CancerData, Homo_sapiens_Data
Author: Shana White
Maintainer: Shana White <vandersm@mail.uc.edu>
git_url: https://git.bioconductor.org/packages/KOdata
git_branch: RELEASE_3_21
git_last_commit: 3119d16
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/KOdata_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: KEGGlincs
dependencyCount: 0
Package: leeBamViews
Version: 1.44.0
Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
Imports: GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
Suggests: biomaRt, org.Sc.sgd.db, edgeR
License: Artistic 2.0
MD5sum: c5ed3c67c98f4d361533403b225b5ffb
NeedsCompilation: no
Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee
2009
Description: data from PMID 19096707; prototype for managing multiple
NGS samples
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data,
SequencingData, RNASeqData, SNPData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/leeBamViews
git_branch: RELEASE_3_21
git_last_commit: 1a0f16f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/leeBamViews_1.44.0.tar.gz
vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf
vignetteTitles: managing multiple NGS samples with bamViews
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R
suggestsMe: EDASeq
dependencyCount: 59
Package: LegATo
Version: 1.2.0
Depends: R (>= 4.4.0)
Imports: animalcules, data.table, dplyr, ggplot2, magrittr,
MultiAssayExperiment, plyr, rlang, S4Vectors, stringr,
SummarizedExperiment, tibble, tidyr, tidyselect
Suggests: BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap,
emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr,
lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling,
TBSignatureProfiler, testthat (>= 3.0.0),
TreeSummarizedExperiment, usethis, vegan
License: MIT + file LICENSE
MD5sum: 1e954d616b2080cf0f09031099f5d1ea
NeedsCompilation: no
Title: LegATo: Longitudinal mEtaGenomic Analysis Toolkit
Description: LegATo is a suite of open-source software tools for
longitudinal microbiome analysis. It is extendable to several
different study forms with optimal ease-of-use for researchers.
Microbiome time-series data presents distinct challenges
including complex covariate dependencies and variety of
longitudinal study designs. This toolkit will allow researchers
to determine which microbial taxa are affected over time by
perturbations such as onset of disease or lifestyle choices,
and to predict the effects of these perturbations over time,
including changes in composition or stability of commensal
bacteria.
biocViews: MicrobiomeData, ReproducibleResearch, SequencingData
Author: Aubrey Odom [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7113-7598>), Yilong Zhang [ctb]
(Author of NMIT functions), Jared Pincus [csl] (ORCID:
<https://orcid.org/0000-0001-6708-5262>, other: Naming
consultant of package), Jordan Pincus [art] (Artist of LegATo
icon)
Maintainer: Aubrey Odom <aodom@bu.edu>
URL: https://wejlab.github.io/LegATo-docs/
VignetteBuilder: knitr
BugReports: https://github.com/wejlab/LegATo/issues
git_url: https://git.bioconductor.org/packages/LegATo
git_branch: RELEASE_3_21
git_last_commit: 7b9a186
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/LegATo_1.2.0.tar.gz
vignettes: vignettes/LegATo/inst/doc/LegATo_vignette.html
vignetteTitles: LegATo Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/LegATo/inst/doc/LegATo_vignette.R
dependencyCount: 191
Package: leukemiasEset
Version: 1.44.0
Depends: R (>= 2.10.1), Biobase (>= 2.5.5)
License: GPL (>= 2)
MD5sum: 9bcc7173eddca96067d8da4a2c6550a6
NeedsCompilation: no
Title: Leukemia's microarray gene expression data (expressionSet).
Description: Expressionset containing gene expresion data from 60 bone
marrow samples of patients with one of the four main types of
leukemia (ALL, AML, CLL, CML) or non-leukemia.
biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData,
LeukemiaCancerData, MicroarrayData, ChipOnChipData,
TissueMicroarrayData, GEO
Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas.
Bioinformatics and Functional Genomics Group. Cancer Research
Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Maintainer: Sara Aibar <saibar@usal.es>
git_url: https://git.bioconductor.org/packages/leukemiasEset
git_branch: RELEASE_3_21
git_last_commit: 15ff27b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/leukemiasEset_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: geNetClassifier, mCSEA, multiclassPairs
dependencyCount: 7
Package: LiebermanAidenHiC2009
Version: 0.46.0
Depends: KernSmooth, IRanges
License: LGPL
MD5sum: ca0a66d6736a445b162708ea1fd8f99e
NeedsCompilation: no
Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in
Science (2009)
Description: This package provides data that were presented in the
article "Comprehensive mapping of long-range interactions
reveals folding principles of the human genome", Science 2009
Oct 9;326(5950):289-93. PMID: 19815776
biocViews: ExperimentData, Genome, SequencingData, DNASeqData,
ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI,
ENCODE
Author: Wolfgang Huber, Felix Klein
Maintainer: Felix Klein <fklein@embl.de>
git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009
git_branch: RELEASE_3_21
git_last_commit: e2a53b6
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/LiebermanAidenHiC2009_0.46.0.tar.gz
vignettes:
vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf
vignetteTitles: Exploration of HiC data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.R
dependencyCount: 10
Package: ListerEtAlBSseq
Version: 1.40.0
Depends: R (>= 3.1.1), methylPipe
Suggests: BSgenome.Hsapiens.UCSC.hg18
License: Artistic 2.0
MD5sum: e0cab1042310224c2dc7921a6fa8d432
NeedsCompilation: no
Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et
al. 2009
Description: Base resolution bisulfite sequencing data of Human DNA
methylomes
biocViews: ExperimentData, Homo_sapiens_Data, SequencingData
Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan
[ctb, cre]
Maintainer: Mattia Furlan <mattia.furlan@iit.it>
git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq
git_branch: RELEASE_3_21
git_last_commit: 8456644
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ListerEtAlBSseq_1.40.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 162
Package: LRcellTypeMarkers
Version: 1.16.0
Depends: R (>= 4.1)
Imports: ExperimentHub
Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat
License: MIT + file LICENSE
MD5sum: f9bcd4092c2b7bc294a78ccdf18388d5
NeedsCompilation: no
Title: Marker gene information for LRcell R Bioconductor package
Description: This is an external ExperimentData package for LRcell.
This data package contains the gene enrichment scores
calculated from scRNA-seq dataset which indicates the gene
enrichment of each cell type in certain brain region. LRcell
package is used to identify specific sub-cell types that drives
the changes observed in a bulk RNA-seq differential gene
expression experiment. For more details, please visit:
https://github.com/marvinquiet/LRcell.
biocViews: ExperimentData, ExperimentHub, RNASeqData, SingleCellData,
ExpressionData, PackageTypeData
Author: Wenjing Ma [cre, aut] (ORCID:
<https://orcid.org/0000-0001-8757-651X>)
Maintainer: Wenjing Ma <wenjing.ma@emory.edu>
VignetteBuilder: knitr
BugReports: https://github.com/marvinquiet/LRcellTypeMarkers/issues
git_url: https://git.bioconductor.org/packages/LRcellTypeMarkers
git_branch: RELEASE_3_21
git_last_commit: e722489
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/LRcellTypeMarkers_1.16.0.tar.gz
vignettes:
vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.html
vignetteTitles: LRcellTypeMarkers: Marker gene information for LRcell R
Bioconductor package using Bioconductor's ExperimentHub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles:
vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.R
suggestsMe: LRcell
dependencyCount: 65
Package: lumiBarnes
Version: 1.48.0
Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0)
License: LGPL
MD5sum: 0c9990f29e6898922bbf6a4acab9e6c9
NeedsCompilation: no
Title: Barnes Benchmark Illumina Tissues Titration Data
Description: The Barnes benchmark dataset can be used to evaluate the
algorithms for Illumina microarrays. It measured a titration
series of two human tissues, blood and placenta, and includes
six samples with the titration ratio of blood and placenta as
100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were
hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate.
The data is loaded as an LumiBatch Object (see documents in the
lumi package).
biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData
Author: Pan Du
Maintainer: Pan Du <dupan@northwestern.edu>
git_url: https://git.bioconductor.org/packages/lumiBarnes
git_branch: RELEASE_3_21
git_last_commit: fbc484c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/lumiBarnes_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayMvout, lumi
dependencyCount: 163
Package: LungCancerACvsSCCGEO
Version: 1.44.0
Depends: R (>= 2.15.0)
License: GPL-2
MD5sum: 8bffc31ebaba11fbe2a955a6ab47d6e9
NeedsCompilation: no
Title: A lung cancer dataset that can be used with maPredictDSC package
for developing outcome prediction models from Affymetrix CEL
files.
Description: This package contains 30 Affymetrix CEL files for 7
Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung
cancer samples taken at random from 3 GEO datasets (GSE10245,
GSE18842 and GSE2109) and other 15 samples from a dataset
produced by the organizers of the IMPROVER Diagnostic Signature
Challenge available from GEO (GSE43580).
biocViews: CancerData, LungCancerData, MicroarrayData, GEO
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
URL: http://bioinformaticsprb.med.wayne.edu/
git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO
git_branch: RELEASE_3_21
git_last_commit: 25b95b1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/LungCancerACvsSCCGEO_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: LungCancerLines
Version: 0.46.0
Imports: Rsamtools
License: Artistic-2.0
MD5sum: b4c1249475bf9f4960f393b2a9f19dee
NeedsCompilation: no
Title: Reads from Two Lung Cancer Cell Lines
Description: Reads from an RNA-seq experiment between two lung cancer
cell lines: H1993 (met) and H2073 (primary). The reads are
stored as Fastq files and are meant for use with the TP53Genome
object in the gmapR package.
biocViews: ExperimentData, Genome, CancerData, LungCancerData,
RNASeqData
Author: Cory Barr, Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
git_url: https://git.bioconductor.org/packages/LungCancerLines
git_branch: RELEASE_3_21
git_last_commit: 12aa3f2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/LungCancerLines_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: gmapR, VariantTools
dependencyCount: 39
Package: lungExpression
Version: 0.46.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5)
License: GPL (>= 2)
MD5sum: c9bb488e5182f12e1e3404e06519890f
NeedsCompilation: no
Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer
Research paper
Description: Data from three large lung cancer studies provided as
ExpressionSets
biocViews: ExperimentData, CancerData, LungCancerData
Author: Robert Scharpf <rscharpf@jhu.edu>, Simens Zhong
<zhong@mts.jhu.edu>, Giovanni Parmigiani <gp@jhu.edu>
Maintainer: Robert Scharpf <rscharpf@jhu.edu>
git_url: https://git.bioconductor.org/packages/lungExpression
git_branch: RELEASE_3_21
git_last_commit: 5d64936
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/lungExpression_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: globaltest
dependencyCount: 7
Package: lydata
Version: 1.34.0
License: MIT + file LICENSE
MD5sum: aecd37c38af5563c9c84ce86a4f61b08
NeedsCompilation: no
Title: Example Dataset for crossmeta Package
Description: Raw data downloaded from GEO for the compound LY294002.
Raw data is from multiple platforms from Affymetrix and
Illumina. This data is used to illustrate the cross-platform
meta-analysis of microarray data using the crossmeta package.
biocViews: ExperimentData, MicroarrayData
Author: Alex Pickering
Maintainer: Alex Pickering <alexvpickering@gmail.com>
git_url: https://git.bioconductor.org/packages/lydata
git_branch: RELEASE_3_21
git_last_commit: f000890
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/lydata_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: ccmap
dependencyCount: 0
Package: M3DExampleData
Version: 1.34.0
Depends: R (>= 3.3)
License: GPL (>=2)
MD5sum: 97044ee2d67e8b64fc8324f5192a8220
NeedsCompilation: no
Title: M3Drop Example Data
Description: Example data for M3Drop package.
biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue,
ExperimentData
Author: Tallulah Andrews <tallulandrews@gmail.com>
Maintainer: Tallulah Andrews <tallulandrews@gmail.com>
git_url: https://git.bioconductor.org/packages/M3DExampleData
git_branch: RELEASE_3_21
git_last_commit: 46aef0f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/M3DExampleData_1.34.0.tar.gz
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: celda, M3Drop
dependencyCount: 0
Package: macrophage
Version: 1.24.0
Depends: R (>= 3.5.0)
Suggests: knitr, markdown
License: GPL (>= 2)
MD5sum: 352177182a7b2b108ca21456cb2e5c18
NeedsCompilation: no
Title: Human macrophage immune response
Description: This package provides the output of running Salmon on a
set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic
effects on chromatin and gene expression indicate a role for
enhancer priming in immune response", published in Nature
Genetics, January 2018. For details on version numbers and how
the samples were processed see the package vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/macrophage
git_branch: RELEASE_3_21
git_last_commit: 8f339a7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/macrophage_1.24.0.tar.gz
vignettes: vignettes/macrophage/inst/doc/macrophage.html
vignetteTitles: Salmon quantifications for human macrophage immune
response experiment
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/macrophage/inst/doc/macrophage.R
suggestsMe: fishpond, GeDi, GeneTonic, mosdef, quantiseqr,
fluentGenomics
dependencyCount: 0
Package: MACSdata
Version: 1.16.0
License: file LICENSE
MD5sum: e256392d760b2bce9465c38ea1bf1b05
NeedsCompilation: no
Title: Test datasets for the MACSr package
Description: Test datasets from the MACS3 test examples are use in the
examples of the `MACSr` package. All 9 datasets are uploaded to
the `ExperimentHub`. The original data can be found at:
https://github.com/macs3-project/MACS/.
biocViews: ExperimentHub, ExperimentData, ChIPSeqData
Author: Qiang Hu [aut, cre]
Maintainer: Qiang Hu <Qiang.Hu@roswellpark.org>
git_url: https://git.bioconductor.org/packages/MACSdata
git_branch: RELEASE_3_21
git_last_commit: 894683e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MACSdata_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: MACSr
dependencyCount: 0
Package: mammaPrintData
Version: 1.44.0
Depends: R (>= 2.13.0)
Suggests: Biobase, readxl, limma
License: Artistic-2.0
MD5sum: e0a3ab909b7f92370835c2d3b5ad6dad
NeedsCompilation: no
Title: RGLists from the Glas and Buyse breast cancer studies
Description: Gene expression data for the two breast cancer cohorts
published by Glas and Buyse in 2006. This cohorts were used to
implement and validate the mammaPrint breast cancer test.
biocViews: ExperimentData, ExpressionData, CancerData,
BreastCancerData, MicroarrayData, TwoChannelData
Author: Luigi Marchionni <marchion@jhu.edu>
Maintainer: Luigi Marchionni <marchion@jhu.edu>
URL: http://luigimarchionni.org/breastTSP.html
git_url: https://git.bioconductor.org/packages/mammaPrintData
git_branch: RELEASE_3_21
git_last_commit: 46ed2ce
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mammaPrintData_1.44.0.tar.gz
vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf
vignetteTitles: Working with the mammaPrintData package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R
dependencyCount: 0
Package: maqcExpression4plex
Version: 1.52.0
Suggests: oligo, pdInfoBuilder
License: GPL
MD5sum: 92d6bba4da0ff02aa1cd5aabc0fa5b47
NeedsCompilation: no
Title: Sample Expression Data - MAQC / HG18 - NimbleGen
Description: Data from human (HG18) 4plex NimbleGen array. It has 24k
genes with 3 60mer probes per gene.
biocViews: ExperimentData, CancerData
Author: NimbleGen Systems
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/maqcExpression4plex
git_branch: RELEASE_3_21
git_last_commit: 7cd26dc
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/maqcExpression4plex_1.52.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligo
dependencyCount: 0
Package: MAQCsubset
Version: 1.46.0
Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi,
methods
Suggests: genefilter, codelink
License: Artistic-2.0
MD5sum: 58623c562ce3c9564b0505d5fc55e82d
NeedsCompilation: no
Title: Experimental Data Package: MAQCsubset
Description: Data Package automatically created on Sun Nov 19 15:59:29
2006.
biocViews: ExperimentData, MicroarrayData, GEO
Author: VJ Carey
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/MAQCsubset
git_branch: RELEASE_3_21
git_last_commit: 37fdb74
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MAQCsubset_1.46.0.tar.gz
vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf
vignetteTitles: MAQC notes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R
suggestsMe: arrayMvout
dependencyCount: 163
Package: marinerData
Version: 1.8.0
Imports: utils, ExperimentHub
Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0)
License: GPL-3
MD5sum: a28af2d4fa0fd17d3f51631db7a9740d
NeedsCompilation: no
Title: ExperimentHub data for the mariner package
Description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion
with an F to S mutated IDR ("FS") or without any mutations to
the IDR ("Wildtype" or "WT"). These files are used for testing
mariner functions and some examples.
biocViews: ExperimentHub, ExperimentData, SequencingData
Author: Eric Davis [aut, cre] (ORCID:
<https://orcid.org/0000-0003-4051-3217>)
Maintainer: Eric Davis <ericscottdavis@outlook.com>
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/marinerData
git_url: https://git.bioconductor.org/packages/marinerData
git_branch: RELEASE_3_21
git_last_commit: 5cadf8a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/marinerData_1.8.0.tar.gz
vignettes: vignettes/marinerData/inst/doc/marinerData.html
vignetteTitles: marinerData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/marinerData/inst/doc/marinerData.R
suggestsMe: mariner
dependencyCount: 65
Package: mCSEAdata
Version: 1.28.0
Depends: R (>= 3.5)
Imports: GenomicRanges
Suggests: BiocStyle, knitr, rmarkdown
License: GPL-2
MD5sum: 3bed6563eae6b3df4047edd3a7ebd506
NeedsCompilation: no
Title: Data package for mCSEA package
Description: Data objects necessary to some mCSEA package functions.
There are also example data objects to illustrate mCSEA package
functionality.
biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData,
ExperimentData
Author: Jordi Martorell Marugán
Maintainer: Jordi Martorell Marugán <jmartorellm@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mCSEAdata
git_branch: RELEASE_3_21
git_last_commit: 479e388
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mCSEAdata_1.28.0.tar.gz
vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.html
vignetteTitles: Data for mCSEA package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R
dependsOnMe: mCSEA
dependencyCount: 23
Package: mcsurvdata
Version: 1.26.0
Depends: R (>= 3.5), ExperimentHub
Imports: AnnotationHub, Biobase
Suggests: BiocStyle, knitr
License: GPL (>=2)
MD5sum: b8e3636e228339ab874bdb73fc34f8b5
NeedsCompilation: no
Title: Meta cohort survival data
Description: This package stores two merged expressionSet objects that
contain the gene expression profile and clinical information of
-a- six breast cancer cohorts and -b- four colorectal cancer
cohorts. Breast cancer data are employed in the vignette of the
hrunbiased package for survival analysis of gene signatures.
biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData
Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo
[aut], Camille Stephan-Otto Attolini [aut]
Maintainer: Adria Caballe Mestres <adria.caballe@irbbarcelona.org>
URL: https://github.com/adricaba/mcsurvdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mcsurvdata
git_branch: RELEASE_3_21
git_last_commit: ee330c9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mcsurvdata_1.26.0.tar.gz
vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html
vignetteTitles: analysis vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R
dependencyCount: 65
Package: MEDIPSData
Version: 1.44.0
Depends: R (>= 3.5.0)
License: GPL (>= 2)
MD5sum: 0db93e67cf0f72ddad7f94e39c01a25f
NeedsCompilation: no
Title: Example data for MEDIPS and QSEA packages
Description: Example data for MEDIPS and QSEA packages, consisting of
chromosome 22 MeDIP and control/Input sample data.
Additionally, the package contains MeDIP seq data from 3 NSCLC
samples and adjacent normal tissue (chr 20-22). All data has
been aligned to human genome hg19.
biocViews: ExperimentData, Genome, SequencingData
Author: Lukas Chavez
Maintainer: Lukas Chavez <lchavez@liai.org>
git_url: https://git.bioconductor.org/packages/MEDIPSData
git_branch: RELEASE_3_21
git_last_commit: 00ebad4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MEDIPSData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MEDIPS, qsea
dependencyCount: 0
Package: MEEBOdata
Version: 1.46.0
License: LGPL
MD5sum: 1df8cd6649a79b44347a1188b8311b6e
NeedsCompilation: no
Title: MEEBO set and MEEBO controls.
Description: R objects describing the MEEBO set.
biocViews: ExperimentData
Author: Agnes Paquet
Maintainer: Agnes Paquet <apaquet@medsfgh.ucsf.edu>
URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/
git_url: https://git.bioconductor.org/packages/MEEBOdata
git_branch: RELEASE_3_21
git_last_commit: 02b916d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MEEBOdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQuality
dependencyCount: 0
Package: MerfishData
Version: 1.10.0
Depends: R (>= 4.2.0), EBImage, SpatialExperiment
Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub,
S4Vectors, SingleCellExperiment, SummarizedExperiment,
HDF5Array
Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore,
terra, testthat, BiocStyle, DropletUtils
License: Artistic-2.0
MD5sum: 5774dc3185c5a2f03a51761d0791c4f5
NeedsCompilation: no
Title: Collection of public MERFISH datasets
Description: MerfishData is an ExperimentHub package that serves
publicly available datasets obtained with Multiplexed
Error-Robust Fluorescence in situ Hybridization (MERFISH).
MERFISH is a massively multiplexed single-molecule imaging
technology capable of simultaneously measuring the copy number
and spatial distribution of hundreds to tens of thousands of
RNA species in individual cells. The scope of the package is to
provide MERFISH data for benchmarking and analysis.
biocViews: ExperimentHub, ExpressionData, HighThroughputImagingData,
Mus_musculus_Data, SingleCellData, SpatialData
Author: Ludwig Geistlinger [aut, cre] (ORCID:
<https://orcid.org/0000-0002-2495-5464>), Tyrone Lee [ctb],
Helena Crowell [ctb] (ORCID:
<https://orcid.org/0000-0002-4801-1767>), Daniela Corbetta
[ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut]
Maintainer: Ludwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>
URL: https://github.com/ccb-hms/MerfishData
VignetteBuilder: knitr
BugReports: https://github.com/ccb-hms/MerfishData/issues
git_url: https://git.bioconductor.org/packages/MerfishData
git_branch: RELEASE_3_21
git_last_commit: 1f488b2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MerfishData_1.10.0.tar.gz
vignettes: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.html,
vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.html,
vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.html
vignetteTitles: Mouse colon ibd, Mouse hypothalamus, Mouse ileum
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.R,
vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.R,
vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.R
dependencyCount: 109
Package: MetaGxBreast
Version: 1.28.0
Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Imports: stats, lattice, impute, SummarizedExperiment
Suggests: testthat, xtable, tinytex
License: Apache License (>= 2)
MD5sum: c034a74761e300e3c653aa6d0e40ed2e
NeedsCompilation: no
Title: Transcriptomic Breast Cancer Datasets
Description: A collection of Breast Cancer Transcriptomic Datasets that
are part of the MetaGxData package compendium.
biocViews: ExpressionData, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData
Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles
[ctb], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
git_url: https://git.bioconductor.org/packages/MetaGxBreast
git_branch: RELEASE_3_21
git_last_commit: 9e95d03
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MetaGxBreast_1.28.0.tar.gz
vignettes: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.pdf
vignetteTitles: MetaGxBreast: a package for breast cancer gene
expression analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.R
dependencyCount: 77
Package: MetaGxOvarian
Version: 1.27.0
Depends: Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R
(>= 3.6.0)
Imports: stats, lattice, impute
Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
License: Artistic-2.0
MD5sum: 3d7c5942d51d8c83bb8ecc7a211cf333
NeedsCompilation: no
Title: Transcriptomic Ovarian Cancer Datasets
Description: A collection of Ovarian Cancer Transcriptomic Datasets
that are part of the MetaGxData package compendium.
biocViews: ExpressionData, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData
Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles
[ctb], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MetaGxOvarian
git_branch: devel
git_last_commit: 7e4535f
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-05
source.ver: src/contrib/MetaGxOvarian_1.27.0.tar.gz
vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.html
vignetteTitles: MetaGxOvarian: A Package for Ovarian Cancer Gene
Expression Analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R
dependencyCount: 77
Package: MetaGxPancreas
Version: 1.27.0
Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
Imports: stats, impute, S4Vectors, AnnotationHub
Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown
License: Artistic-2.0
MD5sum: 37020dd05baabd91369f73ba0cfec062
NeedsCompilation: no
Title: Transcriptomic Pancreatic Cancer Datasets
Description: A collection of pancreatic Cancer transcriptomic datasets
that are part of the MetaGxData package compendium. This
package contains multiple pancreas cancer datasets that have
been downloaded from various resources and turned into
SummarizedExperiment objects. The details of how the authors
normalized the data can be found in the experiment data section
of the objects. Additionally, the location the data was
obtained from can be found in the url variables of the
experiment data portion of each SE.
biocViews: ExpressionData, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData, SequencingData
Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles
[ctb], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MetaGxPancreas
git_branch: devel
git_last_commit: 2c5d902
git_last_commit_date: 2024-10-29
Date/Publication: 2024-11-05
source.ver: src/contrib/MetaGxPancreas_1.27.0.tar.gz
vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.html
vignetteTitles: MetaGxPancreas: A Package for Pancreatic Cancer Gene
Expression Analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R
dependencyCount: 77
Package: metaMSdata
Version: 1.44.0
License: GPL (>= 2)
MD5sum: 7ad6a182e515b06d3f78d3af57055a27
NeedsCompilation: no
Title: Example CDF data for the metaMS package
Description: Example CDF data for the metaMS package
biocViews: ExperimentData, MassSpectrometryData
Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart
[ctb]
Maintainer: Yann Guitton <yann.guitton@gmail.com>
git_url: https://git.bioconductor.org/packages/metaMSdata
git_branch: RELEASE_3_21
git_last_commit: 9ba3cd2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/metaMSdata_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CluMSID, metaMS
dependencyCount: 0
Package: MetaScope
Version: 1.8.1
Depends: R (>= 4.4.0)
Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr,
ggplot2, magrittr, Matrix, MultiAssayExperiment, Rbowtie2,
readr, rlang, Rsamtools, S4Vectors, stringr,
SummarizedExperiment, taxonomizr, tibble, tidyr, tools
Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges,
knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling,
sys, testthat, usethis
Enhances: BiocParallel
License: GPL (>= 3)
MD5sum: 33a1f09c3c4adb8e20f024b55e393779
NeedsCompilation: no
Title: Tools and functions for preprocessing 16S and metagenomic
sequencing microbiome data
Description: This package contains tools and methods for preprocessing
microbiome data. Functionality includes library generation,
demultiplexing, alignment, and microbe identification. It is
in part an R translation of the PathoScope 2.0 pipeline.
biocViews: MicrobiomeData, ReproducibleResearch, SequencingData
Author: Aubrey Odom [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7113-7598>), Sean Lu [aut] (ORCID:
<https://orcid.org/0009-0007-8005-6125>), Rahul Varki [aut]
(ORCID: <https://orcid.org/0009-0003-5721-9484>), W. Evan
Johnson [aut] (ORCID: <https://orcid.org/0000-0002-6247-6595>)
Maintainer: Aubrey Odom <aodom@bu.edu>
URL: https://github.com/wejlab/metascope
https://wejlab.github.io/metascope-docs/
VignetteBuilder: knitr
BugReports: https://github.com/wejlab/MetaScope/issues
git_url: https://git.bioconductor.org/packages/MetaScope
git_branch: RELEASE_3_21
git_last_commit: b713f8c
git_last_commit_date: 2025-05-04
Date/Publication: 2025-05-06
source.ver: src/contrib/MetaScope_1.8.1.tar.gz
vignettes: vignettes/MetaScope/inst/doc/MetaScope_vignette.html
vignetteTitles: "Introduction to MetaScope"
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MetaScope/inst/doc/MetaScope_vignette.R
dependencyCount: 106
Package: MethylAidData
Version: 1.40.0
Depends: MethylAid, R (>= 3.2)
Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
License: GPL (>= 2)
MD5sum: 92d482e118bd25244f21c3b487845e3b
NeedsCompilation: no
Title: MethylAid-summarized data for 2800 Illumina 450k array samples
and 2620 EPIC array samples
Description: A data package containing summarized Illumina 450k array
data on 2800 samples and summarized EPIC data for 2620 samples.
The data can be use as a background data set in the interactive
application.
biocViews: ExperimentData, TechnologyData, MicroarrayData,
MethylationArrayData
Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W.
Holloway, BIOS Consortium, Maarten van Iterson, Faisal I.
Rezwam, Leonard Schalkwyk
Maintainer: M. van Iterson <mviterson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MethylAidData
git_branch: RELEASE_3_21
git_last_commit: dfcde38
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MethylAidData_1.40.0.tar.gz
vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf
vignetteTitles: MethylAid-summarized data on 2800 Illumina 450k array
samples
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MethylAidData/inst/doc/MethylAidData.R
suggestsMe: MethylAid
dependencyCount: 168
Package: methylclockData
Version: 1.16.0
Imports: ExperimentHubData, ExperimentHub, utils
Suggests: knitr, BiocStyle, rmarkdown
License: MIT + file LICENSE
MD5sum: c54973cdd6b007ae1d66a0d509c141f2
NeedsCompilation: no
Title: Data for methylclock package
Description: Collection of 9 datasets, andrews and bakulski cord blood,
blood gse35069, blood gse35069 chen, blood gse35069 complete,
combined cord blood, cord bloo d gse68456, gervin and lyle cord
blood, guintivano dlpfc and saliva gse48472". Data downloaded
from [meffil](https://github.com/perishky/meffil/). Data used
to estimate cell counts using Extrinsic epigenetic age
acceleration (EEAA) method Collection of 12 datasets to use
with MethylClock package to estimate chronological and
gestational DNA methylationwith estimators to use wit different
methylation clocks
biocViews: SpecimenSource, ExperimentHub, Tissue, OrganismData,
Homo_sapiens_Data
Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
URL: https://github.com/isglobal-brge/methylclockData
VignetteBuilder: knitr
BugReports: https://github.com/isglobal-brge/methylclockData/issues
git_url: https://git.bioconductor.org/packages/methylclockData
git_branch: RELEASE_3_21
git_last_commit: d7ae1e2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/methylclockData_1.16.0.tar.gz
vignettes: vignettes/methylclockData/inst/doc/methylcockData.html
vignetteTitles: References for metilclock using Bioconductor's
ExperimentHub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/methylclockData/inst/doc/methylcockData.R
dependsOnMe: methylclock
dependencyCount: 124
Package: MethylSeqData
Version: 1.18.0
Depends: SummarizedExperiment
Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
License: CC0
MD5sum: 3a9002a63218ddbcf372116433530e53
NeedsCompilation: no
Title: Collection of Public DNA Methylation Sequencing Datasets
Description: Base-level (i.e. cytosine-level) counts for a collection
of public bisulfite-seq datasets (e.g., WGBS and RRBS),
provided as SummarizedExperiment objects with sample- and
base-level metadata.
biocViews: ExperimentHub, ExperimentData, SequencingData,
Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData
Author: Peter Hickey [aut, cre]
Maintainer: Peter Hickey <peter.hickey@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MethylSeqData
git_branch: RELEASE_3_21
git_last_commit: bc68b97
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MethylSeqData_1.18.0.tar.gz
vignettes: vignettes/MethylSeqData/inst/doc/MethylSeqData.html
vignetteTitles: User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MethylSeqData/inst/doc/MethylSeqData.R
dependencyCount: 81
Package: MicrobiomeBenchmarkData
Version: 1.10.0
Depends: R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
Imports: BiocFileCache, tools, S4Vectors, ape, utils
Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia,
ggplot2, tidyr, dplyr, magrittr, tibble, purrr
License: Artistic-2.0
MD5sum: d9eeb8e06fb0b5b633008a3d59a5e39e
NeedsCompilation: no
Title: Datasets for benchmarking in microbiome research
Description: The MicrobiomeBenchmarkData package provides functionality
to access microbiome datasets suitable for benchmarking. These
datasets have some biological truth, which allows to have
expected results for comparison. The datasets come from various
published sources and are provided as TreeSummarizedExperiment
objects. Currently, only datasets suitable for benchmarking
differential abundance methods are available.
biocViews: ExperimentData, MicrobiomeData, ReproducibleResearch,
SequencingData
Author: Samuel Gamboa [aut, cre] (ORCID:
<https://orcid.org/0000-0002-6863-7943>), Levi Waldron [aut]
(ORCID: <https://orcid.org/0000-0003-2725-0694>), Marcel Ramos
[ctb]
Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz@gmail.com>
URL: https://github.com/waldronlab/MicrobiomeBenchmarkData,
http://waldronlab.io/MicrobiomeBenchmarkData/
VignetteBuilder: knitr
BugReports:
https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
git_url: https://git.bioconductor.org/packages/MicrobiomeBenchmarkData
git_branch: RELEASE_3_21
git_last_commit: 615e057
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MicrobiomeBenchmarkData_1.10.0.tar.gz
vignettes: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.html,
vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.html,
vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.html
vignetteTitles: Datasets in MicrobiomeBenchmarkData,
MicrobiomeBenchmarkData, Recalibration of the
Stammler_2016_16S_spikein dataset
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.R,
vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.R,
vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.R
suggestsMe: bugphyzz
dependencyCount: 87
Package: microbiomeDataSets
Version: 1.16.0
Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment,
MultiAssayExperiment
Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
License: CC0
MD5sum: 89eabe114dad7e1970301c731428d407
NeedsCompilation: no
Title: Experiment Hub based microbiome datasets
Description: microbiomeDataSets is a collection of microbiome datasets
loaded from Bioconductor'S ExperimentHub infrastructure. The
datasets serve as reference for workflows and vignettes
published adjacent to the microbiome analysis tools on
Bioconductor. Additional datasets can be added overtime and
additions from authors are welcome.
biocViews: ExperimentHub, ExperimentData, MicrobiomeData,
SequencingData
Author: Leo Lahti [cre, aut] (ORCID:
<https://orcid.org/0000-0001-5537-637X>), Felix G.M. Ernst
[aut] (ORCID: <https://orcid.org/0000-0001-5064-0928>),
Sudarshan Shetty [aut] (ORCID:
<https://orcid.org/0000-0001-7280-9915>), Chouaib Benchraka
[ctb] (ORCID: <https://orcid.org/0000-0002-1167-7848>), Yagmur
Simsek [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/microbiomeDataSets
git_branch: RELEASE_3_21
git_last_commit: 5c73287
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/microbiomeDataSets_1.16.0.tar.gz
vignettes:
vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.html
vignetteTitles: microbiomeDataSets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.R
suggestsMe: mia
dependencyCount: 98
Package: microRNAome
Version: 1.30.0
Depends: R (>= 3.5.0), SummarizedExperiment
Suggests: BiocGenerics, RUnit
License: GPL (>= 2)
MD5sum: 8859934f8b7b56128d42779f1beffc2d
NeedsCompilation: no
Title: SummarizedExperiment for the microRNAome project
Description: This package provides a SummarizedExperiment object of
read counts for microRNAs across tissues, cell-types, and
cancer cell-lines. The read count matrix was prepared and
provided by the author of the study: Towards the human cellular
microRNAome.
biocViews: ExperimentData, CellCulture, CancerData, SequencingData,
RNASeqData, miRNAData
Author: Matthew N. McCall <mccallm@gmail.com>, Marc K. Halushka
<mhalush1@jhmi.edu>, Arun H. Patil <arun26feb@gmail.com>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
git_url: https://git.bioconductor.org/packages/microRNAome
git_branch: RELEASE_3_21
git_last_commit: ac499dd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/microRNAome_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 36
Package: minfiData
Version: 0.54.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
License: Artistic-2.0
MD5sum: 5a8376e4b2beb90e49335d7fa11cbd5f
NeedsCompilation: no
Title: Example data for the Illumina Methylation 450k array
Description: Data from 6 samples across 2 groups from 450k methylation
arrays.
biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData
Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
git_url: https://git.bioconductor.org/packages/minfiData
git_branch: RELEASE_3_21
git_last_commit: 71d3467
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/minfiData_0.54.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: methylationArrayAnalysis
suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL,
MethylAid, minfi, missMethyl, MultiDataSet, recountmethylation,
regionalpcs, shinyepico, shinyMethyl, skewr, MethylAidData
dependencyCount: 146
Package: minfiDataEPIC
Version: 1.34.0
Depends: R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
License: Artistic-2.0
MD5sum: 73eef33713c677c4188264ae44dda2e2
NeedsCompilation: no
Title: Example data for the Illumina Methylation EPIC array
Description: Data from 3 technical replicates of the cell line GM12878
from the EPIC methylation array.
biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData
Author: Jean-Philippe Fortin, Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
git_url: https://git.bioconductor.org/packages/minfiDataEPIC
git_branch: RELEASE_3_21
git_last_commit: 2174466
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/minfiDataEPIC_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MethylAid, minfi, recountmethylation, REMP, MethylAidData
dependencyCount: 146
Package: minionSummaryData
Version: 1.38.0
Depends: R (>= 3.2.0)
Suggests: BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 1c6b40098425dabfd5bfe6fae011f47e
NeedsCompilation: no
Title: Summarised MinION sequencing data published by Ashton et al.
2015
Description: Summarised MinION sequencing data for Salmonella Typhi
published by Ashton et al. in 2015. Three replicate runs are
each provided as Fast5Summary objects.
biocViews: ExperimentData, SequencingData
Author: Mike Smith [aut, cre]
Maintainer: Mike Smith <grimbough@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/minionSummaryData
git_branch: RELEASE_3_21
git_last_commit: 01f179b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/minionSummaryData_1.38.0.tar.gz
vignettes:
vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html
vignetteTitles: Creating example MinION summary dataset
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R
suggestsMe: IONiseR
dependencyCount: 0
Package: miRcompData
Version: 1.38.0
Depends: R (>= 3.2),
Imports: utils
License: GPL-3 | file LICENSE
MD5sum: 3937f01289eda62df3a1ee05c28f3ee8
NeedsCompilation: no
Title: Data used in the miRcomp package
Description: Raw amplification data from a large microRNA mixture /
dilution study. These data are used by the miRcomp package to
assess the performance of methods that estimate expression from
the amplification curves.
biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data
Author: Matthew N. McCall <mccallm@gmail.com>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
git_url: https://git.bioconductor.org/packages/miRcompData
git_branch: RELEASE_3_21
git_last_commit: c1dd5a4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/miRcompData_1.38.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: miRcomp
dependencyCount: 1
Package: miRNATarget
Version: 1.46.0
Depends: R (>= 2.10), Biobase
License: GPL
MD5sum: f7618548d7381c91adef778d3980ae49
NeedsCompilation: no
Title: gene target tabale of miRNA for human/mouse used for MiRaGE
package
Description: gene target tabale of miRNA for human/mouse used for
MiRaGE package
biocViews: ExperimentData, Homo_sapiens_Data
Author: Y-h. Taguchi <tag@granular.com>
Maintainer: Y-h. Taguchi <tag@granular.com>
git_url: https://git.bioconductor.org/packages/miRNATarget
git_branch: RELEASE_3_21
git_last_commit: cf3a85a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/miRNATarget_1.46.0.tar.gz
vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf
vignetteTitles: miRNATargetTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R
suggestsMe: MiRaGE
dependencyCount: 7
Package: MMDiffBamSubset
Version: 1.44.0
Suggests: MMDiff2
License: LGPL
MD5sum: 969d42b638d1cd0e05cc995340db9ef7
NeedsCompilation: no
Title: Example ChIP-Seq data for the MMDiff package
Description: Subset of BAM files, including WT_2.bam, Null_2.bam,
Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire
et al., Genes Dev. 2012). Data is available under ArrayExpress
accession numbers E-ERAD-79. Additionally, corresponding subset
of peaks called by MACS
biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data,
DNASeqData, ChIPSeqData, ArrayExpress
Author: Gabriele Schweikert
Maintainer: Gabriele Schweikert <G.Schweikert@ed.ac.uk>
git_url: https://git.bioconductor.org/packages/MMDiffBamSubset
git_branch: RELEASE_3_21
git_last_commit: e3c56ad
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MMDiffBamSubset_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MMDiff2
dependencyCount: 0
Package: MOFAdata
Version: 1.24.0
Depends: R (>= 3.5)
Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle
License: LGPL-3
MD5sum: b3ad33509c675cdb04fede568a7d47a2
NeedsCompilation: yes
Title: Data package for Multi-Omics Factor Analysis (MOFA)
Description: A collection of datasets to accompany the R package MOFA
and illustrate running and analysing MOFA models.
biocViews: ReproducibleResearch
Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian
Buettner, Wolfgang Huber, Oliver Stegle
Maintainer: Britta Velten <britta.velten@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MOFAdata
git_branch: RELEASE_3_21
git_last_commit: 65717db
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MOFAdata_1.24.0.tar.gz
vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html
vignetteTitles: MOFAdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R
importsMe: TDbasedUFE
suggestsMe: TDbasedUFEadv, SUMO
dependencyCount: 0
Package: mosaicsExample
Version: 1.46.0
Depends: R (>= 2.11.1)
License: GPL (>= 2)
MD5sum: 22fbfcd0a292b249d36e7a9590007df1
NeedsCompilation: no
Title: Example data for the mosaics package, which implements MOSAiCS
and MOSAiCS-HMM, a statistical framework to analyze one-sample
or two-sample ChIP-seq data for transcription factor binding
and histone modification
Description: Data for the mosaics package, consisting of (1) chromosome
22 ChIP and control sample data from a ChIP-seq experiment of
STAT1 binding and H3K4me3 modification in MCF7 cell line from
ENCODE database (HG19) and (2) chromosome 21 ChIP and control
sample data from a ChIP-seq experiment of STAT1 binding, with
mappability, GC content, and sequence ambiguity scores of human
genome HG18.
biocViews: ExperimentData, ChIPseqData, Homo_sapiens
Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles
Maintainer: Dongjun Chung <dongjun.chung@gmail.com>
URL: http://groups.google.com/group/mosaics_user_group
git_url: https://git.bioconductor.org/packages/mosaicsExample
git_branch: RELEASE_3_21
git_last_commit: 57de146
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mosaicsExample_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: mosaics
dependencyCount: 0
Package: mouse4302barcodevecs
Version: 1.46.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 2b8cb9f395e65c0d78f8b448e20360cf
NeedsCompilation: no
Title: mouse4302 data for barcode
Description: Data used by the barcode package for microarrays of type
mouse4302.
biocViews: Mus_musculus_Data, MicroarrayData
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs
git_branch: RELEASE_3_21
git_last_commit: 5371a74
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mouse4302barcodevecs_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: MouseAgingData
Version: 1.4.0
Depends: R (>= 4.4.0), SingleCellExperiment
Imports: AnnotationHub, ExperimentHub
Suggests: BiocStyle, knitr, rmarkdown, scater
License: Artistic-2.0
MD5sum: 02e2afea4e7637d605b86da53aff7a78
NeedsCompilation: no
Title: Multi-omics data access for studies investigating the effects of
aging
Description: The MouseAgingData package provides analysis-ready data
resources from different studies focused on aging and
rejuvenation in mice. The package currently provides two 10x
Genomics single-cell RNA-seq datasets. The first study profiled
the aging mouse brain measured across 37,089 cells (Ximerakis
et al., 2019). The second study investigated parabiosis by
profiling a total of 105,329 cells (Ximerakis & Holton et al.,
2023). The datasets are provided as SingleCellExperiment
objects and provide raw UMI counts and cell metadata.
biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData,
SingleCellData, ExperimentHub, PackageTypeData,
Mus_musculus_Data
Author: Tram Nguyen [aut, cre] (ORCID:
<https://orcid.org/0000-0003-4809-6227>), Kris Holton [aut],
Tyrone Lee [aut], Nitesh Turaga [ctb], Ludwig Geistlinger
[aut], Robert Gentleman [aut]
Maintainer: Tram Nguyen <Tram_Nguyen@hms.harvard.edu>
URL: https://github.com/ccb-hms/MouseAgingData
VignetteBuilder: knitr
BugReports: https://github.com/ccb-hms/MouseAgingData/issues
git_url: https://git.bioconductor.org/packages/MouseAgingData
git_branch: RELEASE_3_21
git_last_commit: 63e7dca
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MouseAgingData_1.4.0.tar.gz
vignettes:
vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.html
vignetteTitles: Accessing and Visualizing Parabiosis Droplet Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.R
dependencyCount: 77
Package: MouseGastrulationData
Version: 1.22.0
Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment,
SpatialExperiment
Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix
Suggests: BiocStyle, knitr, rmarkdown, testthat
License: GPL-3
MD5sum: 7e11e826139cd7085e57fe355874676e
NeedsCompilation: no
Title: Single-Cell -omics Data across Mouse Gastrulation and Early
Organogenesis
Description: Provides processed and raw count data for single-cell RNA
sequencing, single-cell ATAC-seq, and seqFISH (spatial
transcriptomic) experiments performed along a timecourse of
mouse gastrulation and early organogenesis.
biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData,
SingleCellData, ExperimentHub, Mus_musculus_Data
Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut]
Maintainer: Jonathan Griffiths <jonathan.griffiths.94@gmail.com>
URL: https://github.com/MarioniLab/MouseGastrulationData
VignetteBuilder: knitr
BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues
git_url: https://git.bioconductor.org/packages/MouseGastrulationData
git_branch: RELEASE_3_21
git_last_commit: 04b7822
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MouseGastrulationData_1.22.0.tar.gz
vignettes:
vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.html
vignetteTitles: Available datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.R
dependsOnMe: OSCA.multisample
suggestsMe: miloR
dependencyCount: 82
Package: MouseThymusAgeing
Version: 1.16.0
Depends: SingleCellExperiment, SummarizedExperiment
Imports: ExperimentHub, methods, BiocGenerics, S4Vectors
Suggests: knitr, scuttle, rmarkdown, BiocStyle
License: GPL-3
MD5sum: 6617f012ee8e6179d9ad70cd75d66867
NeedsCompilation: no
Title: Single-cell Transcriptomics Data of the Ageing Mouse Thymus
Description: This package provides data access to counts matrices and
meta-data for single-cell RNA sequencing data of thymic
epithlial cells across mouse ageing using SMARTseq2 and 10X
Genommics chemistries. Access is provided as a data package via
ExperimentHub. It is designed to facilitate the re-use of data
from Baran-Gale _et al._ in a consistent format that includes
relevant and informative meta-data.
biocViews: ExperimentHub, SingleCellData, ExpressionData,
ExperimentData
Author: Mike Morgan [aut, cre], Jeanette Baran-Gale [aut]
Maintainer: Mike Morgan <michael.morgan@abdn.ac.uk>
VignetteBuilder: knitr
BugReports: https://github.com/MarioniLab/MouseThymusAgeing/issues
git_url: https://git.bioconductor.org/packages/MouseThymusAgeing
git_branch: RELEASE_3_21
git_last_commit: 77e41d1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MouseThymusAgeing_1.16.0.tar.gz
vignettes: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.html
vignetteTitles: Available datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.R
suggestsMe: miloR
dependencyCount: 77
Package: msd16s
Version: 1.28.0
Depends: R (>= 2.10), Biobase, metagenomeSeq,
License: Artistic-2.0
MD5sum: 5537e6da2caf5115a14aa529b10806ad
NeedsCompilation: no
Title: Healthy and moderate to severe diarrhea 16S expression data
Description: Gut 16S sequencing expression data from 992 healthy and
moderate-to-severe diarrhetic samples used in 'Diarrhea in
young children from low-income countries leads to large-scale
alterations in intestinal microbiota composition'.
biocViews: ExperimentData, SequencingData, MicrobiomeData
Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop
Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery
git_url: https://git.bioconductor.org/packages/msd16s
git_branch: RELEASE_3_21
git_last_commit: 440836d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/msd16s_1.28.0.tar.gz
vignettes: vignettes/msd16s/inst/doc/msd16s.pdf
vignetteTitles: msd16s
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/msd16s/inst/doc/msd16s.R
suggestsMe: scTreeViz
dependencyCount: 33
Package: msdata
Version: 0.48.0
Depends: R (>= 3.5.0)
Suggests: xcms, mzR, MSnbase
License: GPL (>= 2)
MD5sum: ab0242b8a187e6823f428e4fe4933f69
NeedsCompilation: no
Title: Various Mass Spectrometry raw data example files
Description: Ion Trap positive ionization mode data in mzML file
format. Subset from 500-850 m/z and 1190-1310 seconds, incl.
MS2 and MS3, intensity threshold 100.000. Extracts from FTICR
Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data,
both mzML and mz5. LC-MSMS and MRM files from proteomics
experiments. PSI mzIdentML example files for various search
engines.
biocViews: ExperimentData, MassSpectrometryData
Author: Steffen Neumann <sneumann@ipb-halle.de>, Laurent Gatto
<laurent.gatto@uclouvain.be> with contriutions from Johannes
Rainer
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>, Laurent Gatto
<laurent.gatto@uclouvain.be>
git_url: https://git.bioconductor.org/packages/msdata
git_branch: RELEASE_3_21
git_last_commit: a257cc3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/msdata_0.48.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: MsQuality
suggestsMe: IPO, koinar, MetaboAnnotation, MsBackendSql, MsExperiment,
MSnbase, mzR, peakPantheR, PSMatch, QFeatures, Spectra,
SpectraQL, TargetDecoy, xcms, RforProteomics
dependencyCount: 0
Package: msigdb
Version: 1.16.0
Depends: R (>= 4.1)
Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db,
AnnotationDbi, methods, stats, AnnotationHub
Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown,
testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
License: CC BY 4.0
MD5sum: 97a672a1a1ea2c84692979d7de5e7c6e
NeedsCompilation: no
Title: An ExperimentHub Package for the Molecular Signatures Database
(MSigDB)
Description: This package provides the Molecular Signatures Database
(MSigDB) in a R accessible objects. Signatures are stored in
GeneSet class objects form the GSEABase package and the entire
database is stored in a GeneSetCollection object. These data
are then hosted on the ExperimentHub. Data used in this package
was obtained from the MSigDB of the Broad Institute. Metadata
for each gene set is stored along with the gene set in the
GeneSet class object.
biocViews: ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data
Author: Dharmesh D. Bhuva [aut, cre] (ORCID:
<https://orcid.org/0000-0002-6398-9157>), Gordon K. Smyth [aut]
(ORCID: <https://orcid.org/0000-0001-9221-2892>), Alexandra
Garnham [aut] (ORCID: <https://orcid.org/0000-0002-8312-8450>)
Maintainer: Dharmesh D. Bhuva <bhuva.d@wehi.edu.au>
URL: https://davislaboratory.github.io/msigdb
VignetteBuilder: knitr
BugReports: https://github.com/DavisLaboratory/msigdb/issues
git_url: https://git.bioconductor.org/packages/msigdb
git_branch: RELEASE_3_21
git_last_commit: d73d327
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/msigdb_1.16.0.tar.gz
vignettes: vignettes/msigdb/inst/doc/msigdb.html
vignetteTitles: msigdb
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/msigdb/inst/doc/msigdb.R
importsMe: escape, mastR, vissE
suggestsMe: epiregulon.extra
dependencyCount: 72
Package: MSMB
Version: 1.26.0
Depends: R (>= 3.5), tibble
Suggests: knitr, BiocStyle
License: LGPL
MD5sum: df91caa55fa6f88bc7c02e751ebf941d
NeedsCompilation: no
Title: Data sets for the book 'Modern Statistics for Biology'
Description: Data sets for the book 'Modern Statistics for Modern
Biology', S.P. Holmes and W. Huber.
biocViews: ExperimentData
Author: Wolfgang Huber, Andrzej Oles, Mike Smith
Maintainer: Wolfgang Huber <wolfgang.huber@embl.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MSMB
git_branch: RELEASE_3_21
git_last_commit: 8c9291f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MSMB_1.26.0.tar.gz
vignettes: vignettes/MSMB/inst/doc/MSMB.html
vignetteTitles: Data sets for the book 'Modern Statistics for Biology'
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MSMB/inst/doc/MSMB.R
dependencyCount: 12
Package: msPurityData
Version: 1.36.0
Suggests: knitr
License: GPL (>= 2)
MD5sum: 6c931fb6523fcf86bb71eaca92cb3ad7
NeedsCompilation: no
Title: Fragmentation spectral libraries and data to test the msPurity
package
Description: Fragmentation spectral libraries and data to test the
msPurity package
biocViews: ExperimentData, MassSpectrometryData
Author: Thomas N. Lawson
Maintainer: Thomas N. Lawson <thomas.nigel.lawson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/msPurityData
git_branch: RELEASE_3_21
git_last_commit: 02a305a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/msPurityData_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: msPurity
dependencyCount: 0
Package: msqc1
Version: 1.36.0
Depends: R (>= 3.6), lattice, stats, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2)
License: GPL
MD5sum: 9337dfbb0065fdab434ae08d07cda169
NeedsCompilation: no
Title: Sigma mix MSQC1 data
Description: contains eight technical replicate data set and a three
replicate dilution series of the MS Qual/Quant Quality Control
Mix standard sample (Sigma-Aldrich, Buchs, Switzerland)
measured on five different mass spectrometer platforms at the
Functional Genomics Center Zurich.
biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch
Author: Tobias Kockmann [aut] (ORCID:
<https://orcid.org/0000-0002-1847-885X>), Christian Trachsel
[aut], Christian Panse [aut, cre] (ORCID:
<https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
URL: https://panoramaweb.org/labkey/MSQC1.url,
http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/msqc1
git_branch: RELEASE_3_21
git_last_commit: 3c9fe74
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/msqc1_1.36.0.tar.gz
vignettes: vignettes/msqc1/inst/doc/poster.pdf,
vignettes/msqc1/inst/doc/chromatography.html,
vignettes/msqc1/inst/doc/msqc1.html
vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number:
282492, LC Observations - Retention Time Stability, Introducing
msqc1 - A Mass Spec Data set for Targeted Proteomics
Performance Evaluation
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/msqc1/inst/doc/chromatography.R,
vignettes/msqc1/inst/doc/msqc1.R,
vignettes/msqc1/inst/doc/poster.R
dependencyCount: 6
Package: mtbls2
Version: 1.37.0
Depends: R (>= 2.10)
Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp, rmarkdown
License: CC0
MD5sum: 8169cded15f702d4bdf53c199018f1e9
NeedsCompilation: no
Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver
nitrate-treated Arabidopsis thaliana leaves of wild-type and
cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)
Description: Indole-3-acetaldoxime (IAOx) represents an early
intermediate of the biosynthesis of a variety of indolic
secondary metabolites including the phytoanticipin
indol-3-ylmethyl glucosinolate and the phytoalexin camalexin
(3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3
double knockout plants are completely impaired in the
conversion of tryptophan to indole-3-acetaldoxime and do not
accumulate IAOx-derived metabolites any longer. Consequently,
comparative analysis of wild-type and cyp79B2 cyp79B3 plant
lines has the potential to explore the complete range of
IAOx-derived indolic secondary metabolites.
biocViews: MassSpectrometryData, RepositoryData
Author: Steffen Neumann <sneumann@ipb-halle.de>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
URL: http://www.ebi.ac.uk/metabolights/MTBLS2,
https://github.com/sneumann/mtbls2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mtbls2
git_branch: devel
git_last_commit: 84dc6ea
git_last_commit_date: 2024-10-29
Date/Publication: 2024-10-31
source.ver: src/contrib/mtbls2_1.37.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: IPO, yamss
dependencyCount: 0
Package: MUGAExampleData
Version: 1.28.0
Depends: R (>= 2.10.0)
License: GPL-3
MD5sum: c69b60762d9ab7f0a8dab8f5b8614390
NeedsCompilation: no
Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome
reconstruction and quantitative trait locus mapping.
Description: This package contains example data for the MUGA array that
is used by the R package DOQTL.
biocViews: ExperimentData, Mus_musculus_Data
Author: Daniel Gatti <Dan.Gatti@jax.org>
Maintainer: Daniel Gatti <Dan.Gatti@jax.org>
git_url: https://git.bioconductor.org/packages/MUGAExampleData
git_branch: RELEASE_3_21
git_last_commit: 89efdba
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/MUGAExampleData_1.28.0.tar.gz
vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf
vignetteTitles: User Manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R
dependencyCount: 0
Package: muleaData
Version: 1.4.0
Suggests: knitr, rmarkdown, ExperimentHub, dplyr
License: MIT + file LICENSE
MD5sum: a7ebfa6c483d03683a4378eabf5a6440
NeedsCompilation: no
Title: Genes Sets for Functional Enrichment Analysis with the 'mulea' R
Package
Description: ExperimentHubData package for the 'mulea' comprehensive
overrepresentation and functional enrichment analyser R
package. Here we provide ontologies (gene sets) in a data.frame
for 27 different organisms, ranging from Escherichia coli to
human, all acquired from publicly available data sources. Each
ontology is provided with multiple gene and protein
identifiers. Please see the NEWS file for a list of changes in
each version.
biocViews: ExperimentData, ExperimentHub, Arabidopsis_thaliana_Data,
Bacillus_subtilis_Data, Caenorhabditis_elegans_Data,
Danio_rerio_Data, Drosophila_melanogaster_Data,
Escherichia_coli_Data, Homo_sapiens_Data, Pan_troglodytes_Data,
Pseudomonas_aeruginosa_Data, Rattus_norvegicus_Data,
Saccharomyces_cerevisiae_Data, Staphylococcus_aureus_Data,
ChIPSeqData, DNASeqData, ExpressionData, miRNAData
Author: Eszter Ari [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7774-1067>), Márton Ölbei [aut]
(ORCID: <https://orcid.org/0000-0002-4903-6237>), Lejla Gul
[aut], Balázs Bohár [aut] (ORCID:
<https://orcid.org/0000-0002-3033-5448>), Tamás Stirling [aut]
(ORCID: <https://orcid.org/0000-0002-8964-6443>)
Maintainer: Eszter Ari <arieszter@gmail.com>
URL: https://github.com/ELTEbioinformatics/muleaData
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/tag/muleaData/issues
git_url: https://git.bioconductor.org/packages/muleaData
git_branch: RELEASE_3_21
git_last_commit: 6d230c1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/muleaData_1.4.0.tar.gz
vignettes: vignettes/muleaData/inst/doc/muleaData.html
vignetteTitles: muleaData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/muleaData/inst/doc/muleaData.R
dependencyCount: 0
Package: multiWGCNAdata
Version: 1.6.0
Depends: ExperimentHub
Imports: utils
Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment
License: Artistic-2.0
MD5sum: 777b4dc10a1cbf3e1b5a9ae05c59f900
NeedsCompilation: no
Title: Data Package for multiWGCNA
Description: Stores expression profiling data from experiments
compatible with the multiWGCNA R package. This includes human
postmortem microarray data from patients and controls
(GSE28521), astrocyte Ribotag RNA-seq data from EAE and
wildtype mice (GSE100329), and mouse RNA-seq data from tau
pathology (rTg4510) and wildtype control mice (GSE125957).
These data can be accessed using the ExperimentHub workflow
(see multiWGCNA vignettes).
biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data,
Mus_musculus_Data, RNASeqData, MicroarrayData
Author: Dario Tommasini [aut, cre] (ORCID:
<https://orcid.org/0000-0002-1214-6547>)
Maintainer: Dario Tommasini <dtommasini0@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/multiWGCNAdata
git_branch: RELEASE_3_21
git_last_commit: 468c769
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/multiWGCNAdata_1.6.0.tar.gz
vignettes: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.html
vignetteTitles: Loading data through ExperimentHub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.R
dependencyCount: 65
Package: muscData
Version: 1.22.0
Depends: R (>= 3.6), ExperimentHub, SingleCellExperiment
Imports: utils
Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
License: MIT + file LICENSE
MD5sum: 9ceebca9b15e7fb390a53b323711a5d0
NeedsCompilation: no
Title: Multi-sample multi-group scRNA-seq data
Description: Data package containing a collection of multi-sample
multi-group scRNA-seq datasets in SingleCellExperiment
Bioconductor object format.
biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO,
Homo_sapiens_Data, ImmunoOncologyData, SingleCellData
Author: Helena L. Crowell [aut, cre]
Maintainer: Helena L. Crowell <helena.crowell@uzh.ch>
URL: https://github.com/HelenaLC/muscData
VignetteBuilder: knitr
BugReports: https://github.com/HelenaLC/muscData/issues
git_url: https://git.bioconductor.org/packages/muscData
git_branch: RELEASE_3_21
git_last_commit: 497deeb
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/muscData_1.22.0.tar.gz
vignettes: vignettes/muscData/inst/doc/muscData.html
vignetteTitles: Multi-sample multi-group scRNA-seq data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/muscData/inst/doc/muscData.R
suggestsMe: dreamlet, glmGamPoi
dependencyCount: 77
Package: muSpaData
Version: 1.0.0
Depends: R (>= 4.5.0), ExperimentHub
Suggests: SpatialExperiment, ggplot2, BiocStyle, knitr, rmarkdown,
R.utils
License: MIT + file LICENSE
MD5sum: 853f4cd71654f0f0b205f75920d2e3fa
NeedsCompilation: no
Title: Multi-sample multi-group spatially resolved transcriptomic data
Description: Data package containing a multi-sample multi-group spatial
dataset in SpatialExperiment Bioconductor object format.
biocViews: ExperimentHub, ExperimentData, ExpressionData, SpatialData,
SingleCellData
Author: Peiying Cai [aut, cre] (ORCID:
<https://orcid.org/0009-0001-9229-2244>)
Maintainer: Peiying Cai <peiying.cai@uzh.ch>
URL: https://github.com/peicai/muSpaData
VignetteBuilder: knitr
BugReports: https://github.com/peicai/muSpaData/issues
git_url: https://git.bioconductor.org/packages/muSpaData
git_branch: RELEASE_3_21
git_last_commit: 5b15b6b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/muSpaData_1.0.0.tar.gz
vignettes: vignettes/muSpaData/inst/doc/muSpaData.html
vignetteTitles: Multi-sample multi-group spatial transcriptomics data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/muSpaData/inst/doc/muSpaData.R
suggestsMe: DESpace
dependencyCount: 65
Package: mvoutData
Version: 1.44.0
Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4),
lumi
License: Artistic-2.0
MD5sum: 19a5b0b629e1f2b0dfe067d192323b6d
NeedsCompilation: no
Title: affy and illumina raw data for assessing outlier detector
performance
Description: affy and illumina raw data for assessing outlier detector
performance
biocViews: ExperimentData, MicroarrayData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/mvoutData
git_branch: RELEASE_3_21
git_last_commit: 8084722
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/mvoutData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayMvout
dependencyCount: 163
Package: NanoporeRNASeq
Version: 1.18.0
Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3)
Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments,
Rsamtools
Enhances: parallel
License: GPL-3 + file LICENSE
MD5sum: 152deaeda3741977a795cc4f234e537b
NeedsCompilation: no
Title: Nanopore RNA-Seq Example data
Description: The NanoporeRNASeq package contains long read RNA-Seq data
generated using Oxford Nanopore Sequencing. The data consists
of 6 samples from two human cell lines (K562 and MCF7) that
were generated by the SG-NEx project. Each of these cell lines
has three replicates, with 1 direct RNA sequencing data and 2
cDNA sequencing data. Reads are aligned to chromosome 22
(Grch38) and stored as bam files. The original data is from the
SG-NEx project.
biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome,
SequencingData
Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut]
Maintainer: Ying Chen <chen_ying@gis.a-star.edu.sg>
URL: https://github.com/GoekeLab/NanoporeRNASeq
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/NanoporeRNASeq
git_branch: RELEASE_3_21
git_last_commit: 73def44
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NanoporeRNASeq_1.18.0.tar.gz
vignettes: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.html
vignetteTitles: NanoporeRNASeq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.R
suggestsMe: bambu
dependencyCount: 65
Package: nanotubes
Version: 1.24.0
Depends: R (>= 3.6)
Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
License: GPL-3
MD5sum: 5a59e57ad55455c347adef217516641f
NeedsCompilation: no
Title: Mouse nanotube CAGE data
Description: Cap Analysis of Gene Expression (CAGE) data from
"Identification of Gene Transcription Start Sites and Enhancers
Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by
Bornholdt et al. supplied as CAGE Transcription Start Sites
(CTSSs).
biocViews: ExperimentData, SequencingData, ExpressionData
Author: Malte Thodberg
Maintainer: Malte Thodberg <maltethodberg@gmail.com>
URL: https://github.com/MalteThodberg/nanotubes
VignetteBuilder: knitr
BugReports: https://github.com/MalteThodberg/nanotubes/issues
git_url: https://git.bioconductor.org/packages/nanotubes
git_branch: RELEASE_3_21
git_last_commit: 0b7ad6e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/nanotubes_1.24.0.tar.gz
vignettes: vignettes/nanotubes/inst/doc/nanotubes.html
vignetteTitles: nanotubes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nanotubes/inst/doc/nanotubes.R
dependsOnMe: CAGEWorkflow
dependencyCount: 0
Package: NCIgraphData
Version: 1.44.0
Depends: R (>= 2.10.0)
Suggests: Rgraphviz
License: GPL-3
MD5sum: 26ec9c2164f1bb7f30c9bad5050d3880
NeedsCompilation: no
Title: Data for the NCIgraph software package
Description: Provides pathways from the NCI Pathways Database as R
graph objects
biocViews: NCI
Author: Laurent Jacob
Maintainer: Laurent Jacob <laurent.jacob@gmail.com>
git_url: https://git.bioconductor.org/packages/NCIgraphData
git_branch: RELEASE_3_21
git_last_commit: 38557fb
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NCIgraphData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: NestLink
Version: 1.24.0
Depends: R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0),
Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4),
ShortRead (>= 1.41)
Imports: grDevices, graphics, stats, utils
Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
License: GPL
MD5sum: d10147bf703b71baed23eccc0a8850fc
NeedsCompilation: no
Title: NestLink an R data package to guide through Engineered Peptide
Barcodes for In-Depth Analyzes of Binding Protein Ensembles
Description: Provides next-generation sequencing (NGS) and mass
spectrometry (MS) sample data, code snippets and replication
material used for developing NestLink. The NestLink approach is
a protein binder selection and identification technology able
to biophysically characterize thousands of library members at
once without handling individual clones at any stage of the
process. Data were acquired on NGS and MS platforms at the
Functional Genomics Center Zurich.
biocViews: ExperimentHub, ExperimentData, SequencingData,
MassSpectrometryData, ReproducibleResearch
Author: Pascal Egloff [aut] (ORCID:
<https://orcid.org/0000-0001-8948-3704>), Iwan Zimmermann [ctb]
(ORCID: <https://orcid.org/0000-0003-3476-4749>), Fabian M.
Arnold [ctb], Cedric A.J. Hutter [ctb] (ORCID:
<https://orcid.org/0000-0002-8920-3343>), Lennart Opitz [aut,
cre] (ORCID: <https://orcid.org/0000-0001-7945-6737>), Lucy
Poveda [ctb] (ORCID: <https://orcid.org/0000-0002-5291-5582>),
Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] (ORCID:
<https://orcid.org/0000-0003-1975-3064>), Bernd Roschitzki
[aut] (ORCID: <https://orcid.org/0000-0001-5756-9773>), Markus
Seeger [aut] (ORCID: <https://orcid.org/0000-0003-1761-8571>)
Maintainer: Lennart Opitz <lopitz@fgcz.ethz.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/NestLink
git_branch: RELEASE_3_21
git_last_commit: 886f69b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NestLink_1.24.0.tar.gz
vignettes:
vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.html,
vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.html,
vignettes/NestLink/inst/doc/link-nanobodies-flycodes.html,
vignettes/NestLink/inst/doc/make-data.html,
vignettes/NestLink/inst/doc/simulate-flycodes.html,
vignettes/NestLink/inst/doc/supplement-note1.html
vignetteTitles: 2. Analyze flycode detectability using ESP and SSRC
prediction, 3. Compare Predicted and Observed flycodes
hydrophobicity values using F255744., 1. Link high quality
flycode and nanobody sequences by NGS filtering., 5. make-data,
0. Simulate flycode properties., 4. Control experiment to
assess the robustness of protein detection via flycodes
(NMETH-A35040 Suppl. notes 1).
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.R,
vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.R,
vignettes/NestLink/inst/doc/link-nanobodies-flycodes.R,
vignettes/NestLink/inst/doc/make-data.R,
vignettes/NestLink/inst/doc/simulate-flycodes.R,
vignettes/NestLink/inst/doc/supplement-note1.R
dependencyCount: 105
Package: NetActivityData
Version: 1.10.0
Depends: R (>= 4.2.0)
Suggests: BiocStyle, knitr
License: MIT + file LICENSE
MD5sum: 60eb4b043fa74b724c9bcfc3bff2723e
NeedsCompilation: no
Title: Data required for getting the gene set scores with NetActivity
package
Description: This package contains the weights from pre-trained shallow
sparsely-connected autoencoders. This data is required for
getting the gene set scores with NetActivity package.
biocViews: ExperimentData, RepositoryData
Author: Carlos Ruiz-Arenas [aut, cre]
Maintainer: Carlos Ruiz-Arenas <carlos.ruiza@upf.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/NetActivityData
git_branch: RELEASE_3_21
git_last_commit: ba38acd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NetActivityData_1.10.0.tar.gz
vignettes: vignettes/NetActivityData/inst/doc/NetActivityData.html
vignetteTitles: "NetActivityData"
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/NetActivityData/inst/doc/NetActivityData.R
importsMe: NetActivity
dependencyCount: 0
Package: Neve2006
Version: 0.46.0
Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
License: Artistic-2.0
MD5sum: fc46585a7810214a5656f2f640e7d8d5
NeedsCompilation: no
Title: expression and CGH data on breast cancer cell lines
Description: Experimental organization of combined expression and CGH
data
biocViews: ExperimentData, CancerData, BreastCancerData
Author: M. Neve et al. in Gray Lab at LBL
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/Neve2006
git_branch: RELEASE_3_21
git_last_commit: 90d2c68
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Neve2006_0.46.0.tar.gz
vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf
vignetteTitles: Neve 2006: combined CGH and expression data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R
dependencyCount: 50
Package: NGScopyData
Version: 1.28.0
License: GPL (>=2)
MD5sum: c1a48467e054783a9b81f73a2af5e141
NeedsCompilation: no
Title: Subset of BAM files of human tumor and pooled normal sequencing
data (Zhao et al. 2014) for the NGScopy package
Description: Subset of BAM files of human lung tumor and pooled normal
samples by targeted panel sequencing. [Zhao et al 2014.
Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using
the University of North Carolina (UNC) Sequencing Assay
Captures Most Previously Described Genetic Aberrations in
NSCLC. In preparation.] Each sample is a 10 percent random
subsample drawn from the original sequencing data. The pooled
normal sample has been rescaled accroding to the total number
of normal samples in the "pool". Here provided is the
subsampled data on chr6 (hg19).
biocViews: ExperimentData, CancerData, LungCancerData, SequencingData
Author: Xiaobei Zhao [aut, cre, cph]
Maintainer: Xiaobei Zhao <xiaobei@binf.ku.dk>
URL:
http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html
git_url: https://git.bioconductor.org/packages/NGScopyData
git_branch: RELEASE_3_21
git_last_commit: 7bbf4de
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NGScopyData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: nullrangesData
Version: 1.14.0
Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet
Imports: utils
Suggests: knitr, rmarkdown
License: GPL-3
MD5sum: 74717a562978e47cd32e954ba63889a6
NeedsCompilation: no
Title: ExperimentHub datasets for the nullranges package
Description: Provides datasets for the nullranges package vignette, in
particular example datasets for DNase hypersensitivity sites
(DHS), CTCF binding sites, and CTCF genomic interactions. These
are used to demonstrate generation of null hypothesis feature
sets, either through block bootstrapping or matching, in the
nullranges vignette. For more details, see the data object man
pages, and the R scripts for object construction provided
within the package.
biocViews: ExperimentHub, Homo_sapiens_Data, SequencingData,
ChIPSeqData, ENCODE
Author: Michael Love [aut, cre] (ORCID:
<https://orcid.org/0000-0001-8401-0545>), Wancen Mu [aut]
(ORCID: <https://orcid.org/0000-0002-5061-7581>), Eric Davis
[aut] (ORCID: <https://orcid.org/0000-0003-4051-3217>), Mikhail
Dozmorov [aut]
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/nullrangesData
git_branch: RELEASE_3_21
git_last_commit: 2f0fed7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/nullrangesData_1.14.0.tar.gz
vignettes: vignettes/nullrangesData/inst/doc/nullrangesData.html
vignetteTitles: nullrangesData package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nullrangesData/inst/doc/nullrangesData.R
suggestsMe: iSEEhub, nullranges
dependencyCount: 78
Package: NxtIRFdata
Version: 1.14.0
Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 4102a11e33c1268633779c9b3dfbb101
NeedsCompilation: no
Title: Data for NxtIRF
Description: NxtIRFdata is a companion package for SpliceWiz, an
interactive analysis and visualization tool for alternative
splicing quantitation (including intron retention) for RNA-seq
BAM files. NxtIRFdata contains Mappability files required for
the generation of human and mouse references. NxtIRFdata also
contains a synthetic genome reference and example BAM files
used to demonstrate SpliceWiz's functionality. BAM files are
based on 6 samples from the Leucegene dataset provided by NCBI
Gene Expression Omnibus under accession number GSE67039.
biocViews: ExperimentData, PackageTypeData, Genome, RNASeqData,
ExpressionData, ExperimentHub
Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb]
Maintainer: Alex Chit Hei Wong <alexchwong.github@gmail.com>
URL: https://github.com/alexchwong/NxtIRFdata
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/
git_url: https://git.bioconductor.org/packages/NxtIRFdata
git_branch: RELEASE_3_21
git_last_commit: eecae18
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/NxtIRFdata_1.14.0.tar.gz
vignettes: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.html
vignetteTitles: NxtIRFdata: a data package for NxtIRF
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.R
dependsOnMe: SpliceWiz
dependencyCount: 98
Package: ObMiTi
Version: 1.16.0
Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub
Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors,
devtools, testthat
License: GPL-3
MD5sum: d71ea8ff668e2146fc13356d68b3c7c9
NeedsCompilation: no
Title: Ob/ob Mice Data on Normal and High Fat Diet
Description: The package provide RNA-seq count for 2 strains of mus
musclus; Wild type and Ob/Ob. Each strain was divided into two
groups, and each group received either chow diet or high fat
diet. RNA expression was measured after 20 weeks in 7 tissues.
biocViews: ExperimentHub, GEO, RNASeqData
Author: Omar Elashkar [aut, cre] (ORCID:
<https://orcid.org/0000-0002-5505-778X>), Mahmoud Ahmed [aut]
(ORCID: <https://orcid.org/0000-0002-4377-6541>)
Maintainer: Omar Elashkar <omar.i.elashkar@gmail.com>
URL: https://github.com/OmarElAshkar/ObMiTi
VignetteBuilder: knitr
BugReports: https://github.com/OmarElAshkar/ObMiTi/issues
git_url: https://git.bioconductor.org/packages/ObMiTi
git_branch: RELEASE_3_21
git_last_commit: 8507da8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ObMiTi_1.16.0.tar.gz
vignettes: vignettes/ObMiTi/inst/doc/ObMiTi.html
vignetteTitles: Using ObMiTi
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ObMiTi/inst/doc/ObMiTi.R
dependencyCount: 76
Package: oct4
Version: 1.24.0
Suggests: knitr, markdown
License: GPL (>= 2)
MD5sum: 77f346847611575f6d93c01a5f2a3949
NeedsCompilation: no
Title: Conditional knockdown of OCT4 in mouse ESCs
Description: This package provides the output of running Salmon on a
set of 12 RNA-seq samples from King & Klose, "The pioneer
factor OCT4 requires the chromatin remodeller BRG1 to support
gene regulatory element function in mouse embryonic stem
cells", published in eLIFE, March 2017. For details on version
numbers and how the samples were processed see the package
vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/oct4
git_branch: RELEASE_3_21
git_last_commit: e82b7a8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/oct4_1.24.0.tar.gz
vignettes: vignettes/oct4/inst/doc/oct4.html
vignetteTitles: Salmon quantifications for condition OCT4 knockdown in
mouse ESCs
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/oct4/inst/doc/oct4.R
dependencyCount: 0
Package: octad.db
Version: 1.10.0
Depends: R (>= 4.2.0), ExperimentHub
Suggests: knitr, rmarkdown
License: Artistic-2.0
MD5sum: c3778b86f1dd1543b6ed21cbc2133f25
NeedsCompilation: no
Title: Open Cancer TherApeutic Discovery (OCTAD) database
Description: Open Cancer TherApeutic Discovery (OCTAD) package implies
sRGES approach for the drug discovery. The essential idea is to
identify drugs that reverse the gene expression signature of a
disease by tamping down over-expressed genes and stimulating
weakly expressed ones. The following package contains all
required precomputed data for whole OCTAD pipeline computation.
biocViews: ExperimentData, CancerData, ExperimentHub, SequencingData,
ExpressionData
Author: E. Chekalin [aut, cre], S. Paithankar [aut], B. Zeng [aut], B.
Glicksberg [ctb], P. Newbury [ctb], J. Xing [ctb], K. Liu
[ctb], A. Wen [ctb], D. Joseph [ctb], B. Chen [aut]
Maintainer: E. Chekalin <eygen.chekalin@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/octad.db
git_branch: RELEASE_3_21
git_last_commit: 8d8ae17
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/octad.db_1.10.0.tar.gz
vignettes: vignettes/octad.db/inst/doc/octad.db.html
vignetteTitles: octad.db
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/octad.db/inst/doc/octad.db.R
dependsOnMe: octad
dependencyCount: 65
Package: OMICsPCAdata
Version: 1.26.0
Depends: R (>= 3.5.0), MultiAssayExperiment
Suggests: knitr, kableExtra, rmarkdown
License: GPL-3
MD5sum: 959ee2bde23446cb26841b86f39e5a81
NeedsCompilation: no
Title: Supporting data for package OMICsPCA
Description: Supporting data for package OMICsPCA
biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData,
ExpressionData, ENCODE
Author: Subhadeep Das
Maintainer: Subhadeep Das <subhadeep1024@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/OMICsPCAdata
git_branch: RELEASE_3_21
git_last_commit: d235e9c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/OMICsPCAdata_1.26.0.tar.gz
vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html
vignetteTitles: OMICsPCAdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R
dependsOnMe: OMICsPCA
dependencyCount: 56
Package: OnassisJavaLibs
Version: 1.30.0
Depends: R (>= 3.4)
Imports: rJava
Suggests: BiocStyle, rmarkdown, knitr
License: GPL-2
MD5sum: c5fe7e6092d5a04464616e0bba56ac61
NeedsCompilation: no
Title: OnassisJavaLibs, java libraries to run conceptmapper and
semantic similarity
Description: A package that contains java libraries to call
conceptmapper and compute semnatic similarity from R
biocViews: ExperimentData
Author: Eugenia Galeota
Maintainer: Eugenia Galeota <eugenia.galeota@gmail.com>
SystemRequirements: Java (>= 1.8)
VignetteBuilder: rmarkdown, knitr
git_url: https://git.bioconductor.org/packages/OnassisJavaLibs
git_branch: RELEASE_3_21
git_last_commit: 7c48ced
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/OnassisJavaLibs_1.30.0.tar.gz
vignettes: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.html
vignetteTitles: OnassisJavaLibs: Java Libraries to support Onassis,,
Ontology Annotation and Semantic Similarity software
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.R
dependencyCount: 2
Package: optimalFlowData
Version: 1.20.0
Depends: R (>= 4.0)
Suggests: knitr, BiocStyle, rmarkdown, magick
License: Artistic-2.0
MD5sum: b56ce226da3054b7786fe9db329906e2
NeedsCompilation: no
Title: optimalFlowData
Description: Data files used as examples and for testing of the
software provided in the optimalFlow package.
biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData,
FlowCytometryData
Author: Hristo Inouzhe <hristo.inouzhe@gmail.com>
Maintainer: Hristo Inouzhe <hristo.inouzhe@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/optimalFlowData
git_branch: RELEASE_3_21
git_last_commit: ba14c09
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/optimalFlowData_1.20.0.tar.gz
vignettes:
vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html
vignetteTitles: optimalFlow: optimal-transport approach to Flow
Cytometry analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R
dependsOnMe: optimalFlow
dependencyCount: 0
Package: orthosData
Version: 1.6.0
Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array,
stringr, SummarizedExperiment
Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat
License: MIT + file LICENSE
MD5sum: 74b90649470abd993229cc80b9e71ea1
NeedsCompilation: no
Title: Data for the orthos package
Description: `orthosData` is the companion ExperimentData package to
the `orthos` R package for mechanistic studies using
differential gene expression experiments. It provides functions
for retrieval from ExperimentHub and local caching of the
models and datasets used internally in orthos.
biocViews: ExperimentData, RNASeqData, ExperimentHub
Author: Panagiotis Papasaikas [aut, cre] (ORCID:
<https://orcid.org/0000-0002-1640-7636>), Charlotte Soneson
[aut] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Michael
Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>),
Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Panagiotis Papasaikas <panagiotis.papasaikas@fmi.ch>
URL: https://github.com/fmicompbio/orthosData
VignetteBuilder: knitr
BugReports: https://github.com/fmicompbio/orthosData/issues
git_url: https://git.bioconductor.org/packages/orthosData
git_branch: RELEASE_3_21
git_last_commit: cd17d97
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/orthosData_1.6.0.tar.gz
vignettes: vignettes/orthosData/inst/doc/orthosData.html
vignetteTitles: 1. Introduction to orthos
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/orthosData/inst/doc/orthosData.R
importsMe: orthos
dependencyCount: 81
Package: parathyroidSE
Version: 1.46.0
Depends: R (>= 3.5.0), SummarizedExperiment
Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
License: LGPL
MD5sum: 3486e101852d90ed86bb746d6d57642c
NeedsCompilation: no
Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of
parathyroid tumors by Haglund et al., J Clin Endocrinol Metab
2012.
Description: This package provides RangedSummarizedExperiment objects
of read counts in genes and exonic parts for paired-end RNA-Seq
data from experiments on primary cultures of parathyroid
tumors. The data were presented in the article "Evidence of a
Functional Estrogen Receptor in Parathyroid Adenomas" by
Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A,
Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab.
jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing
was performed on tumor cultures from 4 patients at 2 time
points over 3 conditions (DPN, OHT and control). One control
sample was omitted by the paper authors due to low quality.
The package vignette describes the creation of the object from
raw sequencing data provided by NCBI Gene Expression Omnibus
under accession number GSE37211. The gene and exon features
are the GRCh37 Ensembl annotations.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/parathyroidSE
git_branch: RELEASE_3_21
git_last_commit: 605e823
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/parathyroidSE_1.46.0.tar.gz
vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
vignetteTitles: parathyroidGenesSE
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R
dependencyCount: 36
Package: pasilla
Version: 1.36.0
Depends: R (>= 3.5.0), DEXSeq
Suggests: rmarkdown, BiocStyle, knitr, roxygen2
License: LGPL
MD5sum: a5c734fa20d78c131d64c27e719428d5
NeedsCompilation: no
Title: Data package with per-exon and per-gene read counts of RNA-seq
samples of Pasilla knock-down by Brooks et al., Genome Research
2011.
Description: This package provides per-exon and per-gene read counts
computed for selected genes from RNA-seq data that were
presented in the article "Conservation of an RNA regulatory map
between Drosophila and mammals" by Brooks AN, Yang L, Duff MO,
Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome
Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232.
The experiment studied the effect of RNAi knockdown of Pasilla,
the Drosophila melanogaster ortholog of mammalian NOVA1 and
NOVA2, on the transcriptome. The package vignette describes
how the data provided here were derived from the RNA-Seq read
sequence data that are provided by NCBI Gene Expression Omnibus
under accession numbers GSM461176 to GSM461181.
biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data,
RNASeqData
Author: Wolfgang Huber, Alejandro Reyes
Maintainer: Alejandro Reyes <alejandro.reyes.ds@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/pasilla
git_branch: RELEASE_3_21
git_last_commit: 1066c5f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pasilla_1.36.0.tar.gz
vignettes: vignettes/pasilla/inst/doc/create_objects.html
vignetteTitles: "Data preprocessing and creation of the data objects
pasillaGenes and pasillaExons"
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pasilla/inst/doc/create_objects.R
importsMe: blacksheepr
suggestsMe: BADER, DEXSeq, EnhancedVolcano, gsean, regionReport,
ReportingTools, tidybulk, pasillaBamSubset
dependencyCount: 115
Package: pasillaBamSubset
Version: 0.46.0
Suggests: pasilla
License: LGPL
MD5sum: 2aae387bc89e01199b562b861498a1d3
NeedsCompilation: no
Title: Subset of BAM files from "Pasilla" experiment
Description: Subset of BAM files untreated1.bam (single-end reads) and
untreated3.bam (paired-end reads) from "Pasilla" experiment
(Pasilla knock-down by Brooks et al., Genome Research 2011).
See the vignette in the pasilla data package for how BAM files
untreated1.bam and untreated3.bam were obtained from the
RNA-Seq read sequence data that is provided by NCBI Gene
Expression Omnibus under accession numbers GSM461176 to
GSM461181. Also contains the DNA sequence for fly chromosome 4
to which the reads can be mapped.
biocViews: ExperimentData, Genome, DNASeqData, RNASeqData
Author: Hervé Pagès
Maintainer: Hervé Pagès <hpages.on.github@gmail.com>
git_url: https://git.bioconductor.org/packages/pasillaBamSubset
git_branch: RELEASE_3_21
git_last_commit: ebf9eaf
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pasillaBamSubset_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: APAlyzer, DEXSeq, GenomicAlignments, GenomicFeatures,
GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges
dependencyCount: 0
Package: PasillaTranscriptExpr
Version: 1.36.0
Depends: R (>= 3.3.0)
Suggests: rtracklayer, BiocStyle, knitr, testthat
License: GPL (>= 3)
MD5sum: cb6d54a8d9e16eff73f59141287848f6
NeedsCompilation: no
Title: Data package with transcript expression obtained with kallisto
from pasilla knock-down RNA-Seq data from Brooks et al.
Description: Provides kallisto workflow and transcript expression of
RNA-Seq data from Brooks et al.
biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData,
ExperimentData, SequencingData, ExpressionData, GEO
Author: Malgorzata Nowicka [aut, cre]
Maintainer: Malgorzata Nowicka <gosia.nowicka@uzh.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr
git_branch: RELEASE_3_21
git_last_commit: a074b67
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PasillaTranscriptExpr_1.36.0.tar.gz
vignettes:
vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.pdf
vignetteTitles: Generation of transcript counts from pasilla dataset
with kallisto
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.R
suggestsMe: DRIMSeq
dependencyCount: 0
Package: PathNetData
Version: 1.44.0
Depends: R (>= 1.14.0)
License: GPL-3
MD5sum: dfce833c79c4664bced6120c9d14976c
NeedsCompilation: no
Title: Experimental data for the PathNet package
Description: This package contains the data employed in the vignette of
the PathNet package. These data belong to the following
publication: PathNet: A tool for pathway analysis using
topological information. Dutta B, Wallqvist A, and Reifman J.,
Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
biocViews: ExperimentData, PathwayInteractionDatabase
Author: Bhaskar Dutta <bhaskar.dutta@gmail.com>, Anders Wallqvist
<awallqvist@bhsai.org>, and Jaques Reifman <jreifman@bhsai.org>
Maintainer: Ludwig Geistlinger <ludwig.geistlinger@gmail.com>
git_url: https://git.bioconductor.org/packages/PathNetData
git_branch: RELEASE_3_21
git_last_commit: cb2ce66
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PathNetData_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PathNet
dependencyCount: 0
Package: PCHiCdata
Version: 1.36.0
Depends: R (>= 3.2), Chicago
Suggests: testthat, BiocStyle, knitr
License: Artistic-2.0
MD5sum: f403ec5657f6262844b46dc5fe46092d
NeedsCompilation: no
Title: Promoter Capture Hi-C data
Description: Subsets of Promoter Capture Hi-C data conveniently
packaged for Chicago users. Data includes interactions detected
for chromosomes 20 and 21 in GM12878 cells and for chromosomes
18 and 19 in mESC.
biocViews: ExperimentData, SequencingData, Homo_sapiens_Data,
Mus_musculus_Data, StemCell
Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett,
Mikhail Spivakov
Maintainer: Mikhail Spivakov <mikhail.spivakov@lms.mrc.ac.uk>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PCHiCdata
git_branch: RELEASE_3_21
git_last_commit: 169ac7b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PCHiCdata_1.36.0.tar.gz
vignettes: vignettes/PCHiCdata/inst/doc/PCHiCdata.html
vignetteTitles: PCHiCdata Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PCHiCdata/inst/doc/PCHiCdata.R
suggestsMe: Chicago
dependencyCount: 75
Package: pd.atdschip.tiling
Version: 0.46.0
Depends: R (>= 3.5.0), methods, RSQLite (>= 0.10.0), oligoClasses (>=
1.15.58), oligo (>= 1.17.3), DBI
Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
License: Artistic-2.0
MD5sum: 536589a25f1a0a12f814c8b3745153ff
NeedsCompilation: no
Title: Platform Design Info for Affymetrix Atdschip_tiling
Description: Platform Design Info for Affymetrix Atdschip_tiling
biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData
Author: Kristof De Beuf
Maintainer: Kristof De Beuf <kristof.debeuf@ugent.be>
git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling
git_branch: RELEASE_3_21
git_last_commit: 64c4c69
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pd.atdschip.tiling_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 64
Package: pepDat
Version: 1.28.0
Depends: R (>= 3.5.0)
Imports: GenomicRanges
Suggests: knitr
License: Artistic-2.0
MD5sum: 729d4deeadc8682e4e0a79ad946a0a08
NeedsCompilation: no
Title: Peptide microarray data package
Description: Provides sample files and data for the vignettes of
pepStat and Pviz as well as peptide collections for HIV and
SIV.
biocViews: MicroarrayData
Author: Renan Sauteraud, Raphael Gottardo
Maintainer: Renan Sauteraud <rsautera@fhcrc.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/pepDat
git_branch: RELEASE_3_21
git_last_commit: 4c98752
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pepDat_1.28.0.tar.gz
vignettes: vignettes/pepDat/inst/doc/pepDat.pdf
vignetteTitles: The pepDat users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pepDat/inst/doc/pepDat.R
suggestsMe: pepStat, Pviz
dependencyCount: 23
Package: PepsNMRData
Version: 1.26.0
Depends: R (>= 3.5)
Suggests: knitr, markdown, rmarkdown, BiocStyle
License: GPL-2 | file LICENSE
MD5sum: 7eebf2ac221cfb9e01ff6944ff813563
NeedsCompilation: no
Title: Datasets for the PepsNMR package
Description: This package contains all the datasets used in the PepsNMR
package.
biocViews: ExperimentData, OrganismData, Homo_sapiens_Data
Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal
de Tullio [dtc]
Maintainer: Manon Martin <manon.martin@uclouvain.be>
BugReports: https://github.com/ManonMartin/PepsNMRData/issues
git_url: https://git.bioconductor.org/packages/PepsNMRData
git_branch: RELEASE_3_21
git_last_commit: 25fc7f2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PepsNMRData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: PepsNMR
dependencyCount: 0
Package: PhyloProfileData
Version: 1.22.1
Depends: R (>= 4.4.0)
Imports: ExperimentHub, Biostrings, BiocStyle
Suggests: knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 844f225330299cd953d2d008f6e6afae
NeedsCompilation: yes
Title: Data package for phylogenetic profile analysis using
PhyloProfile tool
Description: Two experimental datasets to illustrate running and
analysing phylogenetic profiles with PhyloProfile package.
biocViews: ExperimentData, ReproducibleResearch, ExperimentHub
Author: Vinh Tran [aut, cre] (ORCID:
<https://orcid.org/0000-0001-6772-7595>), Ingo Ebersberger
[aut], Hannah Mülbaier [ctb], Arpit Jain [ctb]
Maintainer: Vinh Tran <tran@bio.uni-frankfurt.de>
URL: https://github.com/BIONF/PhyloProfileData
VignetteBuilder: knitr
BugReports: https://github.com/trvinh/PhyloProfileData/issues
git_url: https://git.bioconductor.org/packages/PhyloProfileData
git_branch: RELEASE_3_21
git_last_commit: f34ab36
git_last_commit_date: 2025-06-18
Date/Publication: 2025-06-19
source.ver: src/contrib/PhyloProfileData_1.22.1.tar.gz
vignettes: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.html
vignetteTitles: PhyloProfileData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.R
dependencyCount: 81
Package: plotgardenerData
Version: 1.14.0
Depends: R (>= 4.1.0)
Suggests: rmarkdown, knitr
License: MIT + file LICENSE
MD5sum: 89cc9c857786846bfd20a956929b4232
NeedsCompilation: no
Title: Datasets and test data files for the plotgardener package
Description: This is a supplemental data package for the plotgardener
package. Includes example datasets used in plotgardener
vignettes and example raw data files. For details on how to use
these datasets, see the plotgardener package vignettes.
biocViews: ExperimentData, Homo_sapiens_Data, ExpressionData, Genome,
ChIPSeqData, ENCODE
Author: Nicole Kramer [aut, cre] (ORCID:
<https://orcid.org/0000-0001-9617-9671>)
Maintainer: Nicole Kramer <nekramer@live.unc.edu>
URL: https://github.com/PhanstielLab/plotgardenerData,
https://phanstiellab.github.io/plotgardener
VignetteBuilder: knitr
BugReports: https://github.com/PhanstielLab/plotgardenerData/issues
git_url: https://git.bioconductor.org/packages/plotgardenerData
git_branch: RELEASE_3_21
git_last_commit: df1f4e9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/plotgardenerData_1.14.0.tar.gz
vignettes: vignettes/plotgardenerData/inst/doc/plotgardenerData.html
vignetteTitles: plotgardenerData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/plotgardenerData/inst/doc/plotgardenerData.R
suggestsMe: plotgardener
dependencyCount: 0
Package: prebsdata
Version: 1.44.0
Depends: R (>= 2.14.0)
License: Artistic-2.0
MD5sum: 1a0a9e3becab9633e105d9836015de25
NeedsCompilation: no
Title: Data for 'prebs' package
Description: This package contains data required to run examples in
'prebs' package. The data files include: 1) Small sample bam
files for demonstration purposes 2) Probe sequence mappings for
Custom CDF (taken from
http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp)
3) Probe sequence mappings for manufacturer's CDF (manually
created using bowtie)
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Karolis Uziela and Antti Honkela
Maintainer: Karolis Uziela <karolis.uziela@scilifelab.se>
git_url: https://git.bioconductor.org/packages/prebsdata
git_branch: RELEASE_3_21
git_last_commit: 562e2ca
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prebsdata_1.44.0.tar.gz
vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf
vignetteTitles: prebsdata User Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: prebs, SigFuge
dependencyCount: 0
Package: preciseTADhub
Version: 1.16.0
Depends: R (>= 4.1)
Imports: ExperimentHub
Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD
License: MIT + file LICENSE
MD5sum: f2fc7d1e0d7a57422e72b1fb59095292
NeedsCompilation: no
Title: Pre-trained random forest models obtained using preciseTAD
Description: An experimentdata package to supplement the preciseTAD
package containing pre-trained models and the variable
importances of each genomic annotation used to build the model
parsed into list objects and available in ExperimentHub. In
total, preciseTADhub provides access to n=84 random forest
classification models optimized to predict TAD/chromatin loop
boundary regions and stored as .RDS files. The value, n, comes
from the fact that we considered l=2 cell lines {GM12878,
K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and
c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting
CHR9). Furthermore, each object is itself a two-item list
containing: (1) the model object, and (2) the variable
importances for CTCF, RAD21, SMC3, and ZNF143 used to predict
boundary regions. Each model is trained via a "holdout"
strategy, in which data from chromosomes {CHR1, CHR2, ...,
CHRi-1, CHRi+1, ..., CHR22} were used to build the model and
the ith chromosome was reserved for testing. See
https://doi.org/10.1101/2020.09.03.282186 for more detail on
the model building strategy.
biocViews: ExperimentData, PackageTypeData, ExperimentHub, Genome
Author: Spiro Stilianoudakis [aut], Mikhail Dozmorov [aut, cre]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
URL: https://github.com/dozmorovlab/preciseTADhub
VignetteBuilder: knitr
BugReports: https://github.com/dozmorovlab/preciseTADhub/issues
git_url: https://git.bioconductor.org/packages/preciseTADhub
git_branch: RELEASE_3_21
git_last_commit: 139271c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/preciseTADhub_1.16.0.tar.gz
vignettes: vignettes/preciseTADhub/inst/doc/preciseTADhub.html
vignetteTitles: preciseTADhub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/preciseTADhub/inst/doc/preciseTADhub.R
dependencyCount: 65
Package: PREDAsampledata
Version: 0.48.0
Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
Suggests: hgu133plus2.db, hgu133plus2cdf
License: Artistic-2.0
MD5sum: 6c20adc0dd0e5a50352b20f244f338a4
NeedsCompilation: no
Title: expression and copy number data on clear cell renal carcinoma
samples
Description: Sample data for PREDA package. (annotations objects
synchronized with GeneAnnot custom CDFs version 2.2.0)
biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData,
MicroarrayData, TissueMicroarrayData, ArrayExpress
Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan
Maintainer: Francesco Ferrari <francesco.ferrari@ifom.eu>
git_url: https://git.bioconductor.org/packages/PREDAsampledata
git_branch: RELEASE_3_21
git_last_commit: dca0d31
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PREDAsampledata_0.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PREDA
dependencyCount: 62
Package: ProData
Version: 1.46.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5)
License: GPL
MD5sum: 03e0699476fec3473e50b6b19f0c8f8d
NeedsCompilation: no
Title: SELDI-TOF data of Breast cancer samples
Description: A data package of SELDI-TOF protein mass spectrometry data
of 167 breast cancer and normal samples.
biocViews: ExperimentData, CancerData, BreastCancerData,
MassSpectrometryData, NCI
Author: Xiaochun Li
Maintainer: Xiaochun Li <xiaochun@jimmy.harvard.edu>
git_url: https://git.bioconductor.org/packages/ProData
git_branch: RELEASE_3_21
git_last_commit: 3c08517
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ProData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CorrectedFDR
dependencyCount: 7
Package: pRolocdata
Version: 1.46.0
Depends: R (>= 3.6.3), MSnbase
Imports: Biobase, utils
Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment
License: GPL-2
MD5sum: e217ea5ab1b36862973db5694f80d8d6
NeedsCompilation: no
Title: Data accompanying the pRoloc package
Description: Mass-spectrometry based spatial proteomics data sets and
protein complex separation data. Also contains the time course
expression experiment from Mulvey et al. 2015.
biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData,
Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data,
Mus_musculus_Data, StemCell, Proteome
Author: Laurent Gatto [aut] (ORCID:
<https://orcid.org/0000-0002-1520-2268>), Oliver Crook [aut]
(ORCID: <https://orcid.org/0000-0001-5669-8506>), Lisa Breckels
[cre, aut] (ORCID: <https://orcid.org/0000-0001-8918-7171>)
Maintainer: Lisa Breckels <lms79@cam.ac.uk>
URL: https://github.com/lgatto/pRolocdata
BugReports: https://github.com/lgatto/pRolocdata/issues
git_url: https://git.bioconductor.org/packages/pRolocdata
git_branch: RELEASE_3_21
git_last_commit: e326d80
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pRolocdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: bandle
suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics
dependencyCount: 135
Package: prostateCancerCamcap
Version: 1.36.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: 41606eedcf7f54d718f065b963528ce9
NeedsCompilation: no
Title: Prostate Cancer Data
Description: A Bioconductor data package for the Ross-Adams (2015)
Prostate Cancer dataset.
biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData,
CancerData, ProstateCancerData
Author: Mark Dunning
Maintainer: Mark Dunning <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerCamcap
git_branch: RELEASE_3_21
git_last_commit: d185f4f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prostateCancerCamcap_1.36.0.tar.gz
vignettes:
vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.pdf
vignetteTitles: prostateCancerCamcap
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.R
dependencyCount: 7
Package: prostateCancerGrasso
Version: 1.36.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: fc44f08142293a60f3a156430aa99695
NeedsCompilation: no
Title: Prostate Cancer Data
Description: A Bioconductor data package for the Grasso (2012) Prostate
Cancer dataset.
biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData,
CancerData, ProstateCancerData
Author: Mark Dunning
Maintainer: Mark Dunning <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerGrasso
git_branch: RELEASE_3_21
git_last_commit: ce14be7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prostateCancerGrasso_1.36.0.tar.gz
vignettes:
vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.pdf
vignetteTitles: prostateCancerGrasso
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.R
dependencyCount: 7
Package: prostateCancerStockholm
Version: 1.36.0
Depends: Biobase , R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: b79294dbdfe9cf93fdf3513ad965e56a
NeedsCompilation: no
Title: Prostate Cancer Data
Description: A Bioconductor data package for the Stockholm dataset
biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData,
CancerData, ProstateCancerData
Author: Mark Dunning
Maintainer: Mark Dunning <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerStockholm
git_branch: RELEASE_3_21
git_last_commit: c6c3cd5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prostateCancerStockholm_1.36.0.tar.gz
vignettes:
vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.pdf
vignetteTitles: prostateCancerStockholm
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.R
dependencyCount: 7
Package: prostateCancerTaylor
Version: 1.36.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery, org.Hs.eg.db
License: Artistic-2.0
MD5sum: 61f3b815424304c9860ff8882148610d
NeedsCompilation: no
Title: Prostate Cancer Data
Description: A Bioconductor data package for the Taylor et al (2010)
dataset.
biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData,
CancerData, ProstateCancerData
Author: Mark Dunning
Maintainer: Mark Dunning <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerTaylor
git_branch: RELEASE_3_21
git_last_commit: 2597f83
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prostateCancerTaylor_1.36.0.tar.gz
vignettes:
vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.pdf
vignetteTitles: prostateCancerTaylor
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.R
dependencyCount: 7
Package: prostateCancerVarambally
Version: 1.36.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: a4cfcf6a7f11ba724c6350ed21ec1889
NeedsCompilation: no
Title: Prostate Cancer Data
Description: A Bioconductor data package for the Varambally dataset
biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData,
CancerData, ProstateCancerData
Author: Mark Dunning
Maintainer: Mark Dunning <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerVarambally
git_branch: RELEASE_3_21
git_last_commit: 73f630d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/prostateCancerVarambally_1.36.0.tar.gz
vignettes:
vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.pdf
vignetteTitles: prostateCancerVarambally
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.R
dependencyCount: 7
Package: ProteinGymR
Version: 1.2.1
Depends: R (>= 4.4.0)
Imports: ExperimentHub, AnnotationHub, bio3d, r3dmol, ggExtra, dplyr,
forcats, ggdist, gghalves, ggplot2, pals, purrr, queryup, spdl,
tidyr, tidyselect, ComplexHeatmap, circlize, stringr,
lifecycle, rlang, htmltools
Suggests: tibble, BiocStyle, knitr, testthat (>= 3.0.0)
License: Artistic-2.0
MD5sum: d4dff0636799f98a50255bc5be2c2c15
NeedsCompilation: no
Title: Programmatic access to ProteinGym datasets in R/Bioconductor
Description: The ProteinGymR package provides analysis-ready data
resources from ProteinGym, generated by Notin et al., 2023, as
well as built-in functionality to visualize the data.
ProteinGym comprises a collection of benchmarks for evaluating
the performance of models predicting the effect of point
mutations. This package provides access to 1. deep mutational
scanning (DMS) scores from 217 assays measuring the impact of
all possible amino acid substitutions across 186 proteins, 2.
model performance metrics and prediction scores from 79 variant
prediction models in the zero-shot setting and 12 models in the
semi-supervised setting.
biocViews: ExperimentData, ExperimentHub, PackageTypeData,
Homo_sapiens_Data, ReproducibleResearch, CellCulture,
SequencingData, Proteome
Author: Tram Nguyen [aut, cre] (ORCID:
<https://orcid.org/0000-0003-4809-6227>), Pascal Notin [aut],
Aaron Kollasch [aut], Debora Marks [aut], Ludwig Geistlinger
[aut]
Maintainer: Tram Nguyen <Tram_Nguyen@hms.harvard.edu>
URL: https://github.com/ccb-hms/ProteinGymR
VignetteBuilder: knitr
BugReports: https://github.com/ccb-hms/ProteinGymR/issues
git_url: https://git.bioconductor.org/packages/ProteinGymR
git_branch: RELEASE_3_21
git_last_commit: 0b34428
git_last_commit_date: 2025-06-02
Date/Publication: 2025-06-10
source.ver: src/contrib/ProteinGymR_1.2.1.tar.gz
vignettes:
vignettes/ProteinGymR/inst/doc/data_import_and_representation.html,
vignettes/ProteinGymR/inst/doc/visualization_exploration.html
vignetteTitles: Data access and representation, Visualization and
exploration"
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/ProteinGymR/inst/doc/data_import_and_representation.R,
vignettes/ProteinGymR/inst/doc/visualization_exploration.R
dependencyCount: 137
Package: ptairData
Version: 1.16.0
Imports: rhdf5, signal, stats, graphics
Suggests: knitr, rmarkdown, testthat, BiocStyle
License: GPL-3
MD5sum: 839945c4cb5f2302af2bbf74256db0b1
NeedsCompilation: no
Title: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell
culture headspace
Description: The package ptairData contains two raw datasets from
Proton-Transfer-Reaction Time-of-Flight mass spectrometer
acquisitions (PTR-TOF-MS), in the HDF5 format. One from the
exhaled air of two volunteer healthy individuals with three
replicates, and one from the cell culture headspace from two
mycobacteria species and one control (culture medium only) with
two replicates. Those datasets are used in the examples and in
the vignette of the ptairMS package (PTR-TOF-MS data
pre-processing). There are also used to gererate the ptrSet in
the ptairMS data : exhaledPtrset and mycobacteriaSet
biocViews: ExperimentData, MassSpectrometryData, CellCulture
Author: camille Roquencourt [aut, cre]
Maintainer: camille Roquencourt <camille.roquencourt@hotmail.fr>
VignetteBuilder: knitr
BugReports: https://github.com/camilleroquencourt/ptairData/issues
git_url: https://git.bioconductor.org/packages/ptairData
git_branch: RELEASE_3_21
git_last_commit: ad6240f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ptairData_1.16.0.tar.gz
vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html
vignetteTitles: PTR-TOF-MS dataset
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R
suggestsMe: ptairMS
dependencyCount: 10
Package: PtH2O2lipids
Version: 1.34.0
Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
Suggests: gplots, RColorBrewer, cluster, vegan
License: MIT + file LICENSE
MD5sum: 3e46d388f9b4f114ccb4d8527f5635c2
NeedsCompilation: no
Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al.
(2015)
Description: Annotated HPLC-ESI-MS lipid data in positive ionization
mode from an experiment in which cultures of the marine diatom
Phaeodactylum tricornutum were treated with various
concentrations of hydrogen peroxide (H2O2) to induce oxidative
stress. The experiment is described in Graff van Creveld, et
al., 2015, "Early perturbation in mitochondria redox
homeostasis in response to environmental stress predicts cell
fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists
of two objects: A CAMERA xsAnnotate object
(ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object
(ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative
compound assignments from the default LOBSTAHS database. Isomer
annotation is recorded in three other LOBSet slots.
biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData,
Phaeodactylum_tricornutum_data
Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut],
Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut],
James Collins [cre]
Maintainer: James Collins <james.r.collins@aya.yale.edu>
URL: http://dx.doi.org/10.1038/ismej.2014.136,
https://github.com/vanmooylipidomics/PtH2O2lipids,
http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529
BugReports:
https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new
git_url: https://git.bioconductor.org/packages/PtH2O2lipids
git_branch: RELEASE_3_21
git_last_commit: aff5d44
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PtH2O2lipids_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: LOBSTAHS
dependencyCount: 159
Package: pumadata
Version: 2.44.0
Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0)
License: LGPL
MD5sum: 5ecd738bc80cc2d6ba8bb107ad3fb7b7
NeedsCompilation: no
Title: Various data sets for use with the puma package
Description: This is a simple data package including various data sets
derived from the estrogen data for use with the puma
(Propagating Uncertainty in Microarray Analysis) package.
biocViews: ExperimentData, MicroarrayData, SNPData
Author: Richard Pearson
Maintainer: Xuejun liu <xuejun.liu@nuaa.edu.cn>
URL: http://umber.sbs.man.ac.uk/resources/puma
git_url: https://git.bioconductor.org/packages/pumadata
git_branch: RELEASE_3_21
git_last_commit: 5c3b82f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/pumadata_2.44.0.tar.gz
vignettes: vignettes/pumadata/inst/doc/pumadata.pdf
vignetteTitles: pumadata User Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pumadata/inst/doc/pumadata.R
suggestsMe: puma
dependencyCount: 67
Package: PWMEnrich.Dmelanogaster.background
Version: 4.42.0
Depends: R (>= 2.10), methods, PWMEnrich
License: GPL-3
MD5sum: bd29bfef4485a99a7c2a207739a81619
NeedsCompilation: no
Title: D. melanogaster background for PWMEnrich
Description: PWMEnrich pre-compiled background objects for Drosophila
melanogaster and MotifDb D. melanogaster motifs.
biocViews: Drosophila_melanogaster_Data
Author: Robert Stojnic
Maintainer: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background
git_branch: RELEASE_3_21
git_last_commit: cad267f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver:
src/contrib/PWMEnrich.Dmelanogaster.background_4.42.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 31
Package: PWMEnrich.Hsapiens.background
Version: 4.42.0
Depends: R (>= 2.10), methods, PWMEnrich
License: GPL-3
MD5sum: 2d7844cb58057cf00381836fdf386f86
NeedsCompilation: no
Title: H. sapiens background for PWMEnrich
Description: PWMEnrich pre-compiled background objects for H. sapiens
(human) and MotifDb H. sapiens motifs.
biocViews: Homo_sapiens_Data, CGHData
Author: Robert Stojnic
Maintainer: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background
git_branch: RELEASE_3_21
git_last_commit: b8d9eb1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.42.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 31
Package: PWMEnrich.Mmusculus.background
Version: 4.42.0
Depends: R (>= 2.10), methods, PWMEnrich
License: GPL-3
MD5sum: f3bfe1e81b6e71e41aa53ab110eb51f0
NeedsCompilation: no
Title: M. musculus background for PWMEnrich
Description: PWMEnrich pre-compiled background objects for M.musculus
(mouse) and MotifDb M. musculus motifs.
biocViews: Mus_musculus_Data
Author: Robert Stojnic
Maintainer: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background
git_branch: RELEASE_3_21
git_last_commit: e4310d9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.42.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 31
Package: QDNAseq.hg19
Version: 1.38.0
Depends: R (>= 3.2.1), QDNAseq
License: GPL
MD5sum: e6281801bc4ad0746c202944c04d06c3
NeedsCompilation: no
Title: QDNAseq bin annotation for hg19
Description: This package provides QDNAseq bin annotations for the
human genome build hg19.
biocViews: ExperimentData, OrganismData, Homo_sapiens_Data
Author: Daoud Sie [aut, cre]
Maintainer: Daoud Sie <d.sie@vumc.nl>
URL: https://github.com/tgac-vumc/QDNAseq.hg19
BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues
git_url: https://git.bioconductor.org/packages/QDNAseq.hg19
git_branch: RELEASE_3_21
git_last_commit: f1e95f0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/QDNAseq.hg19_1.38.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biscuiteer, QDNAseq
dependencyCount: 59
Package: QDNAseq.mm10
Version: 1.38.0
Depends: R (>= 3.2.1), QDNAseq
License: GPL
MD5sum: 0485b5bce82bc57f0fbd662ab0071053
NeedsCompilation: no
Title: Bin annotation mm10
Description: This package provides QDNAseq bin annotations for the
mouse genome build mm10.
biocViews: ExperimentData, OrganismData, Mus_musculus_Data
Author: Daoud Sie [aut, cre]
Maintainer: Daoud Sie <d.sie@vumc.nl>
URL: https://github.com/tgac-vumc/QDNAseq.mm10
BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues
git_url: https://git.bioconductor.org/packages/QDNAseq.mm10
git_branch: RELEASE_3_21
git_last_commit: 8be83a6
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/QDNAseq.mm10_1.38.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biscuiteer, QDNAseq
dependencyCount: 59
Package: qPLEXdata
Version: 1.26.0
Depends: R (>= 3.5), qPLEXanalyzer
Imports: utils, knitr, MSnbase, dplyr
Suggests: statmod
License: GPL-2
MD5sum: 51b842bdae1a5da72defb0dc718d9d47
NeedsCompilation: no
Title: Data accompanying qPLEXanalyzer package
Description: qPLEX-RIME and Full proteome TMT mass spectrometry
datasets.
biocViews: ExperimentData, MassSpectrometryData, Proteome
Author: Kamal Kishore Developer [aut, cre]
Maintainer: Kamal Kishore Developer <kamal.fartiyal84@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/qPLEXdata
git_branch: RELEASE_3_21
git_last_commit: d03cb23
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/qPLEXdata_1.26.0.tar.gz
vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf
vignetteTitles: qPLEXdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R
suggestsMe: qPLEXanalyzer
dependencyCount: 148
Package: QUBICdata
Version: 1.36.0
Depends: R (>= 3.1)
Suggests: knitr, rmarkdown
License: Unlimited | file LICENSE
MD5sum: 64dfcb47c02df9362320f4c065598c5c
NeedsCompilation: no
Title: Data employed in the vignette of the QUBIC package
Description: The data employed in the vignette of the QUBIC package.
These data belong to Many Microbe Microarrays Database and
STRING v10.
biocViews: Escherichia_coli_Data, OrganismData, ExperimentData
Author: Yu Zhang [aut, cre], Qin Ma [aut]
Maintainer: Yu Zhang <zy26@jlu.edu.cn>
URL: http://github.com/zy26/QUBICdata
VignetteBuilder: knitr
BugReports: http://github.com/zy26/QUBICdata/issues
git_url: https://git.bioconductor.org/packages/QUBICdata
git_branch: RELEASE_3_21
git_last_commit: 6de85a4
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/QUBICdata_1.36.0.tar.gz
vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf
vignetteTitles: QUBIC Data Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R
suggestsMe: QUBIC
dependencyCount: 0
Package: raerdata
Version: 1.6.0
Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer,
SingleCellExperiment
Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
License: MIT + file LICENSE
MD5sum: 195e10ffc826cf8f63d55f1364fc2741
NeedsCompilation: no
Title: A collection of datasets for use with raer package
Description: raerdata is an ExperimentHub package that provides a
collection of files useful for demostrating functionality in
the raer package. Datasets include 10x genomics scRNA-seq, bulk
RNA-seq, and paired whole-genome and RNA-seq data. Additionally
databases of human and mouse RNA editing sites are provided.
biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub,
PackageTypeData, ExpressionData
Author: Kent Riemondy [aut, cre] (ORCID:
<https://orcid.org/0000-0003-0750-1273>)
Maintainer: Kent Riemondy <kent.riemondy@cuanschutz.edu>
URL: https://github.com/rnabioco/raerdata
VignetteBuilder: knitr
BugReports: https://github.com/rnabioco/raerdata/issues
git_url: https://git.bioconductor.org/packages/raerdata
git_branch: RELEASE_3_21
git_last_commit: c3157b1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/raerdata_1.6.0.tar.gz
vignettes: vignettes/raerdata/inst/doc/raerdata.html
vignetteTitles: raerdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/raerdata/inst/doc/raerdata.R
suggestsMe: raer
dependencyCount: 96
Package: rcellminerData
Version: 2.30.0
Depends: R (>= 3.5.0), Biobase
Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown
License: LGPL-3 + file LICENSE
MD5sum: 6bc940852ed3da54df8e3a6de983f9cf
NeedsCompilation: no
Title: rcellminerData: Molecular Profiles and Drug Response for the
NCI-60 Cell Lines
Description: The NCI-60 cancer cell line panel has been used over the
course of several decades as an anti-cancer drug screen. This
panel was developed as part of the Developmental Therapeutics
Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National
Cancer Institute (NCI). Thousands of compounds have been tested
on the NCI-60, which have been extensively characterized by
many platforms for gene and protein expression, copy number,
mutation, and others (Reinhold, et al., 2012). The purpose of
the CellMiner project (http://discover.nci.nih.gov/ cellminer)
has been to integrate data from multiple platforms used to
analyze the NCI-60 and to provide a powerful suite of tools for
exploration of NCI-60 data.
biocViews: CancerData, CopyNumberVariationData, ExpressionData,
SNPData, NCI, MicroarrayData, miRNAData
Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>, Vinodh Rajapakse
<vinodh.rajapakse@nih.gov>, Fathi Elloumi
<fathi.elloumi@nih.gov>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/rcellminerData
git_branch: RELEASE_3_21
git_last_commit: d109b27
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/rcellminerData_2.30.0.tar.gz
vignettes: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.html
vignetteTitles: Accessing CellMiner Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.R
dependsOnMe: rcellminer
dependencyCount: 7
Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp
Version: 1.28.0
Depends: R (>= 3.3)
Imports: data.table
License: GPL-3
MD5sum: b0e5c5f81922eb8efe39f49628366fc2
NeedsCompilation: no
Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k
motifs
Description: RcisTarget databases: Gene-based motif rankings and
annotation to transcription factors. This package contains a
subset of 4.6k motifs (cisbp motifs), scored only within 500bp
upstream and the TSS. See RcisTarget tutorial to download the
full databases, containing 20k motifs and search space up to
10kbp around the TSS.
biocViews: Homo_sapiens_Data
Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of
Computational Biology, KU Leuven Center for Human Genetics.
Leuven, Belgium.
Maintainer: Sara Aibar <sara.aibar@kuleuven.vib.be>
URL: http://scenic.aertslab.org
git_url:
https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp
git_branch: RELEASE_3_21
git_last_commit: 6030af7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver:
src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RcisTarget
dependencyCount: 2
Package: ReactomeGSA.data
Version: 1.22.0
Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
License: Artistic-2.0
MD5sum: 5be76df4bef3fb05a33b5d2d846ea1c2
NeedsCompilation: no
Title: Companion data package for the ReactomeGSA package
Description: Companion data sets to showcase the functionality of the
ReactomeGSA package. This package contains proteomics and
RNA-seq data of the melanoma B-cell induction study by Griss et
al. and scRNA-seq data from Jerby-Arnon et al.
biocViews: ExpressionData, RNASeqData, Proteome, Homo_sapiens_Data
Author: Johannes Griss [aut, cre] (ORCID:
<https://orcid.org/0000-0003-2206-9511>)
Maintainer: Johannes Griss <johannes.griss@meduniwien.ac.at>
URL: https://github.com/reactome/ReactomeGSA.data/issues
BugReports: https://github.com/reactome/ReactomeGSA.data
git_url: https://git.bioconductor.org/packages/ReactomeGSA.data
git_branch: RELEASE_3_21
git_last_commit: 54a560d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/ReactomeGSA.data_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ReactomeGSA
dependencyCount: 186
Package: RegParallel
Version: 1.26.0
Depends: doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
License: GPL-3
MD5sum: aac9d36159a2a5df4d050d0db2f262d1
NeedsCompilation: no
Title: Standard regression functions in R enabled for parallel
processing over large data-frames
Description: In many analyses, a large amount of variables have to be
tested independently against the trait/endpoint of interest,
and also adjusted for covariates and confounding factors at the
same time. The major bottleneck in these is the amount of time
that it takes to complete these analyses. With RegParallel, a
large number of tests can be performed simultaneously. On a
12-core system, 144 variables can be tested simultaneously,
with 1000s of variables processed in a matter of seconds via
'nested' parallel processing. Works for logistic regression,
linear regression, conditional logistic regression, Cox
proportional hazards and survival models, and Bayesian logistic
regression. Also caters for generalised linear models that
utilise survey weights created by the 'survey' CRAN package and
that utilise 'survey::svyglm'.
biocViews: DiseaseModel
Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su
[aut]
Maintainer: Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
URL: https://github.com/kevinblighe/RegParallel
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RegParallel
git_branch: RELEASE_3_21
git_last_commit: a5a9950
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RegParallel_1.26.0.tar.gz
vignettes: vignettes/RegParallel/inst/doc/RegParallel.html
vignetteTitles: Standard regression functions in R enabled for parallel
processing over large data-frames
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R
dependencyCount: 39
Package: RforProteomics
Version: 1.46.0
Depends: R (>= 3.5), MSnbase (>= 2.5.3)
Imports: R.utils, biocViews, BiocManager
Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown,
BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12),
MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR,
SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db,
e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable,
lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA,
DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram,
protViz, genefilter, plotly, gridExtra, dplyr, lubridate,
magick, cleaver
License: Artistic-2.0
MD5sum: 0e42356a5235e0387af1a75fac53391e
NeedsCompilation: no
Title: Companion package to the 'Using R and Bioconductor for
proteomics data analysis' publication
Description: This package contains code to illustrate the 'Using R and
Bioconductor for proteomics data analysis' and 'Visualisation
of proteomics data using R and Bioconductor' manuscripts. The
vignettes describe the code and data needed to reproduce the
examples and figures described in the paper and functionality
for proteomics visualisation. It also contain various function
to discover R software for mass spectrometry and proteomics.
biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch
Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk
[ctb], Thomas Pedersen Lin [ctb]
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
URL: http://lgatto.github.com/RforProteomics/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RforProteomics
git_branch: RELEASE_3_21
git_last_commit: 7cbb19e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RforProteomics_1.46.0.tar.gz
vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html,
vignettes/RforProteomics/inst/doc/RProtVis.html
vignetteTitles: Using R for proteomics data analysis, Visualisation of
proteomics data using R and Bioconductor
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R,
vignettes/RforProteomics/inst/doc/RProtVis.R
suggestsMe: MSstatsQC
dependencyCount: 144
Package: RGMQLlib
Version: 1.28.0
Depends: R(>= 3.4.2)
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: 4239e78c53f27d0b1e336ddce84a5b24
NeedsCompilation: no
Title: RGMQLlib, java libraries to run GMQL scala API
Description: A package that contains scala libraries to call GMQL from
R used by RGMQL package. It contains a scalable data management
engine written in Scala programming language.
biocViews: ExperimentData,RepositoryData
Author: Simone Pallotta [aut, cre], Marco Masseroli [aut]
Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RGMQLlib
git_branch: RELEASE_3_21
git_last_commit: 939d464
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RGMQLlib_1.28.0.tar.gz
vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf
vignetteTitles: RGMQLlib: scala Libraries to support GMQL
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: rheumaticConditionWOLLBOLD
Version: 1.46.0
Depends: R (>= 2.10.0)
Suggests: genefilter, Biobase, hgu133plus2.db
License: Artistic-2.0
MD5sum: 0e6ba0df0d826fe8ed1b6cf0b82b38a2
NeedsCompilation: no
Title: Normalized gene expression dataset published by Wollbold et al.
[2009] (WOLLBOLD).
Description: Normalized gene expression data from rheumatic diseases
from study published by Wollbold et al. in 2009, provided as an
eSet.
biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData,
ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress
Author: Alejandro Quiroz-Zarate, John Quackenbush
Maintainer: Alejandro Quiroz-Zarate <aquiroz@hsph.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url:
https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD
git_branch: RELEASE_3_21
git_last_commit: 56fba5f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: RITANdata
Version: 1.32.0
Depends: R (>= 4.2)
Suggests: knitr
License: file LICENSE
MD5sum: b88ca49dc419bc7657725fd9a71194e2
NeedsCompilation: no
Title: This package contains reference annotation and network data sets
Description: Data such as is contained in the two R data files in this
package are required for the RITAN package examples. Users are
highly encouraged to use their own or additional resources in
conjunction with RITANdata. See the RITAN vignettes and
RITAN.md for more information, such as gathering more
up-to-date annotation data.
biocViews: AnnotationData, Homo_sapiens
Author: Michael Zimmermann [aut, cre]
Maintainer: Michael Zimmermann <mtzimmermann@mcw.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RITANdata
git_branch: RELEASE_3_21
git_last_commit: 53c0601
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RITANdata_1.32.0.tar.gz
vignettes: vignettes/RITANdata/inst/doc/RITANdata.html
vignetteTitles: Vignette Title
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/RITANdata/inst/doc/RITANdata.R
importsMe: RITAN
dependencyCount: 0
Package: RMassBankData
Version: 1.46.0
Suggests: RMassBank
License: Artistic-2.0
MD5sum: f691839a388049b4e79a5eb16ab385a3
NeedsCompilation: no
Title: Test dataset for RMassBank
Description: Example spectra, example compound list(s) and an example
annotation list for a narcotics dataset; required to test
RMassBank. The package is described in the man page for
RMassBankData. Includes new XCMS test data.
biocViews: ExperimentData, MassSpectrometryData
Author: Michael Stravs, Emma Schymanski, Steffen Neumann
Maintainer: Michael Stravs, Emma Schymanski <massbank@eawag.ch>
git_url: https://git.bioconductor.org/packages/RMassBankData
git_branch: RELEASE_3_21
git_last_commit: 3235785
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RMassBankData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RMassBank
dependencyCount: 0
Package: RNAmodR.Data
Version: 1.22.0
Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
Imports: utils
Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
License: Artistic-2.0
MD5sum: 8d43a49cc4995884667b7ac9e6f344da
NeedsCompilation: no
Title: Example data for the RNAmodR package
Description: RNAmodR.Data contains example data, which is used for
vignettes and example workflows in the RNAmodR and dependent
packages.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd]
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>
URL: https://github.com/FelixErnst/RNAmodR.Data
VignetteBuilder: knitr
BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues
git_url: https://git.bioconductor.org/packages/RNAmodR.Data
git_branch: RELEASE_3_21
git_last_commit: 34d455a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RNAmodR.Data_1.22.0.tar.gz
vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html
vignetteTitles: RNAmodR.Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R
suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML,
RNAmodR.RiboMethSeq
dependencyCount: 124
Package: RNAseqData.HNRNPC.bam.chr14
Version: 0.46.0
Suggests: GenomicAlignments, BiocManager
License: LGPL
MD5sum: 0b0f9e9d438589978c9257a7bb0621c3
NeedsCompilation: no
Title: Aligned reads from RNAseq experiment: Transcription profiling by
high throughput sequencing of HNRNPC knockdown and control HeLa
cells
Description: The package contains 8 BAM files, 1 per sequencing run.
Each BAM file was obtained by (1) aligning the reads
(paired-end) to the full hg19 genome with TopHat2, and then (2)
subsetting to keep only alignments on chr14. See accession
number E-MTAB-1147 in the ArrayExpress database for details
about the experiment, including links to the published study
(by Zarnack et al., 2012) and to the FASTQ files.
biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData,
GEO, NCI, RNASeqData, ArrayExpress
Author: Hervé Pagès
Maintainer: Hervé Pagès <hpages.on.github@gmail.com>
URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/
git_url:
https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14
git_branch: RELEASE_3_21
git_last_commit: 0282a21
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: sequencing
suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles,
GenomicRanges, roar, Rsamtools, SplicingGraphs
dependencyCount: 0
Package: RnaSeqSampleSizeData
Version: 1.40.0
Depends: edgeR,R (>= 2.10)
Suggests: BiocStyle, knitr
License: GPL (>= 2)
MD5sum: bb3d12d9797fa8889b21695181b82f4d
NeedsCompilation: no
Title: RnaSeqSampleSizeData
Description: RnaSeqSampleSizeData package provides the read counts and
dispersion distribution from real RNA-seq experiments. It can
be used by RnaSeqSampleSize package to estimate sample size and
power for RNA-seq experiment design.
biocViews: ExperimentData, CancerData, RNASeqData
Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao <zhaoshilin@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData
git_branch: RELEASE_3_21
git_last_commit: 5acfecf
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnaSeqSampleSizeData_1.40.0.tar.gz
vignettes:
vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf
vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion
distribution from real data for sample size estimation of
RNA-seq experiments
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.R
dependsOnMe: RnaSeqSampleSize
dependencyCount: 11
Package: RnBeads.hg19
Version: 1.40.0
Depends: R (>= 3.5.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: e01b6d2f363c32c902cc83c68266a360
NeedsCompilation: no
Title: RnBeads.hg19
Description: Automatically generated RnBeads annotation package for the
assembly hg19.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.hg19
git_branch: RELEASE_3_21
git_last_commit: f7ea44b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnBeads.hg19_1.40.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: MAGAR
suggestsMe: RnBeads
dependencyCount: 23
Package: RnBeads.hg38
Version: 1.40.0
Depends: R (>= 3.5.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: ad843b83e315495484ca8b7ad42e6e20
NeedsCompilation: no
Title: RnBeads.hg38
Description: RnBeads annotation package for the assembly hg38.
Author: RnBeads Team
Maintainer: RnBeads Team <team@rnbeads.org>
git_url: https://git.bioconductor.org/packages/RnBeads.hg38
git_branch: RELEASE_3_21
git_last_commit: 47bab6c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnBeads.hg38_1.40.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: MAGAR
suggestsMe: RnBeads
dependencyCount: 23
Package: RnBeads.mm10
Version: 2.16.0
Depends: R (>= 3.5.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: be55e33be3335ae99326a5c8e2718c6c
NeedsCompilation: no
Title: RnBeads.mm10
Description: Automatically generated RnBeads annotation package for the
assembly mm10.
Author: RnBeads Team
Maintainer: RnBeads Team <team@rnbeads.org>
git_url: https://git.bioconductor.org/packages/RnBeads.mm10
git_branch: RELEASE_3_21
git_last_commit: ab7a2a9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnBeads.mm10_2.16.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 23
Package: RnBeads.mm9
Version: 1.40.0
Depends: R (>= 3.5.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: 7c8b7bdd7ab9c74bb1c4ebec5b63d94f
NeedsCompilation: no
Title: RnBeads.mm9
Description: Automatically generated RnBeads annotation package for the
assembly mm9.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.mm9
git_branch: RELEASE_3_21
git_last_commit: c515f02
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnBeads.mm9_1.40.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RnBeads
dependencyCount: 23
Package: RnBeads.rn5
Version: 1.40.0
Depends: R (>= 3.5.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: fd4ef4eac4ab8e106c68bae9790afc39
NeedsCompilation: no
Title: RnBeads.rn5
Description: Automatically generated RnBeads annotation package for the
assembly rn5.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.rn5
git_branch: RELEASE_3_21
git_last_commit: 2533d7f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RnBeads.rn5_1.40.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 23
Package: RRBSdata
Version: 1.28.0
Depends: R (>= 3.5.0), BiSeq (>= 1.9.2)
License: LGPL-3
MD5sum: 22d82273bec2158c0be72a4c2b9f0a38
NeedsCompilation: no
Title: An RRBS data set with 12 samples and 10,000 simulated DMRs
Description: RRBS data set comprising 12 samples with simulated
differentially methylated regions (DMRs).
biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData
Author: Katja Hebestreit, Hans-Ulrich Klein
Maintainer: Katja Hebestreit <katja.hebestreit@gmail.com>
git_url: https://git.bioconductor.org/packages/RRBSdata
git_branch: RELEASE_3_21
git_last_commit: 77bb5d5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RRBSdata_1.28.0.tar.gz
vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf
vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated
DMRs.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R
dependencyCount: 92
Package: rRDPData
Version: 1.28.0
Depends: rRDP
License: GPL-2
MD5sum: aed90134596628a27299e9a101ce55ee
NeedsCompilation: no
Title: Databases for the Default RDP Classifier
Description: The package provides the data for the RDP Classifier 2.14
released in August 2023. It contains the latest bacterial and
archaeal taxonomy training set No. 19 as described in Wang Q,
Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more
accurate taxonomic classification. Microbiol Resour Announc
0:e01063-23. <doi.org/10.1128/mra.01063-23>
biocViews: SequencingData, MicrobiomeData, RNASeqData
Author: Michael Hahsler [aut, cre] (ORCID:
<https://orcid.org/0000-0003-2716-1405>), Nagar Anurag [aut]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
URL: https://github.com/mhahsler/rRDP
git_url: https://git.bioconductor.org/packages/rRDPData
git_branch: RELEASE_3_21
git_last_commit: b06d16c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/rRDPData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: rRDP
dependencyCount: 27
Package: RTCGA.clinical
Version: 20151101.38.0
Depends: R (>= 3.2.0), RTCGA
Suggests: rmarkdown, knitr
License: GPL-2
MD5sum: 960807ffdc5f7235d7d124dc082b5779
NeedsCompilation: no
Title: Clinical datasets from The Cancer Genome Atlas Project
Description: Package provides clinical datasets from The Cancer Genome
Atlas Project for all cohorts types from
http://gdac.broadinstitute.org/. Clinical data format is
explained here
https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview.
Data from 2015-11-01 snapshot.
biocViews: Annotation Data
Author: Marcin Kosinski <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.clinical
git_branch: RELEASE_3_21
git_last_commit: 39abc65
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.clinical_20151101.38.0.tar.gz
vignettes:
vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html
vignetteTitles: Using RTCGA to download clinical data as included in
RTCGA.clinical
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R
suggestsMe: RTCGA, TDbasedUFEadv
dependencyCount: 130
Package: RTCGA.CNV
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: a8531159a66f2fd25af0840d6451cfd1
NeedsCompilation: no
Title: CNV (Copy-number variation) datasets from The Cancer Genome
Atlas Project
Description: Package provides CNV (based on Merge snp) datasets from
The Cancer Genome Atlas Project for all cohorts types from
http://gdac.broadinstitute.org/. Data format is explained here
https://wiki.nci.nih.gov/display/TCGA/Retrieving
+Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.
biocViews: AnnotationData
Author: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.CNV
git_branch: RELEASE_3_21
git_last_commit: b68d798
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.CNV_1.36.0.tar.gz
vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html,
vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html
vignetteTitles: Using RTCGA to download CNV data as included in
RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R,
vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RTCGA.methylation
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 693fabfc0dd7ad945f96c92887129ea7
NeedsCompilation: no
Title: Methylation datasets from The Cancer Genome Atlas Project
Description: Package provides methylation (humanmethylation27) datasets
from The Cancer Genome Atlas Project for all available cohorts
types from http://gdac.broadinstitute.org/. Data format is
explained here
https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from
2015-11-01 snapshot.
biocViews: AnnotationData
Author: Marcin Kosinski [aut, cre], Witold Chodor [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.methylation
git_branch: RELEASE_3_21
git_last_commit: 5fa177a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.methylation_1.36.0.tar.gz
vignettes:
vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html
vignetteTitles: Using RTCGA to download methylation data as included in
RTCGA.methylation
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RTCGA.miRNASeq
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: b40916fa4cd686159a9a15e796f8ef4e
NeedsCompilation: no
Title: miRNASeq datasets from The Cancer Genome Atlas Project
Description: Package provides miRNASeq datasets from The Cancer Genome
Atlas Project for all available cohorts types from
http://gdac.broadinstitute.org/. Data format is explained here
https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview
Data from 2015-11-01 snapshot.
biocViews: AnnotationData
Author: Witold Chodor <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq
git_branch: RELEASE_3_21
git_last_commit: d189b24
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.miRNASeq_1.36.0.tar.gz
vignettes:
vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html
vignetteTitles: Using RTCGA to download miRNASeq data as included in
RTCGA.miRNASeq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RTCGA.mRNA
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 0a5319858849fec3a79aac0e7f0136dd
NeedsCompilation: no
Title: mRNA datasets from The Cancer Genome Atlas Project
Description: Package provides mRNA datasets from The Cancer Genome
Atlas Project for all available cohorts types from
http://gdac.broadinstitute.org/. Data format is explained here
https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data
from 2015-11-01 snapshot.
biocViews: AnnotationData
Author: Witold Chodor <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.mRNA
git_branch: RELEASE_3_21
git_last_commit: 91cd9ce
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.mRNA_1.36.0.tar.gz
vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html
vignetteTitles: Using RTCGA to download mRNA data as included in
RTCGA.mRNA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RTCGA.mutations
Version: 20151101.38.0
Depends: R (>= 3.2.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 2891220f4094c8ea936dc0071204d734
NeedsCompilation: no
Title: Mutations datasets from The Cancer Genome Atlas Project
Description: Package provides mutations datasets from The Cancer Genome
Atlas Project for all cohorts types from
http://gdac.broadinstitute.org/. Mutations data format is
explained here
https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification.
There is extra one column with patients' barcodes. Data from
2015-11-01 snapshot.
biocViews: Annotation Data
Author: Marcin Kosinski <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.mutations
git_branch: RELEASE_3_21
git_last_commit: 1d21fef
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.mutations_20151101.38.0.tar.gz
vignettes:
vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html
vignetteTitles: Using RTCGA to download mutations data as included in
RTCGA.mutations
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RTCGA.PANCAN12
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 2e6e291783471ae5e5de974c76fe9d44
NeedsCompilation: no
Title: PanCan 12 from Genome Cancer Browser
Description: Package provides clinical, expression, cnv and mutation
data from Genome Cancer Browser.
biocViews: AnnotationData
Author: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12
git_branch: RELEASE_3_21
git_last_commit: 71404f2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.PANCAN12_1.36.0.tar.gz
vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html
vignetteTitles: Using RTCGA.PANCAN12 to compare time to death
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R
suggestsMe: GOpro
dependencyCount: 130
Package: RTCGA.rnaseq
Version: 20151101.38.0
Depends: R (>= 3.2.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 7f5192626c84c23a8d19c5099bfa9927
NeedsCompilation: no
Title: Rna-seq datasets from The Cancer Genome Atlas Project
Description: Package provides rna-seq datasets from The Cancer Genome
Atlas Project for all cohorts types from
http://gdac.broadinstitute.org/. Rna-seq data format is
explained here
https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data
source is illumina hiseq Level 3 RSEM normalized expression
data. Data from 2015-11-01 snapshot.
biocViews: Annotation Data
Author: Marcin Kosinski <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq
git_branch: RELEASE_3_21
git_last_commit: 0d4b3ee
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.rnaseq_20151101.38.0.tar.gz
vignettes:
vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html
vignetteTitles: Using RTCGA to download RNAseq data as included in
RTCGA.rnaseq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R
suggestsMe: RTCGA, TDbasedUFEadv, FSelectorRcpp
dependencyCount: 130
Package: RTCGA.RPPA
Version: 1.36.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr, rmarkdown
License: GPL-2
MD5sum: 1d217aa454b9f5f39497e062250d76a9
NeedsCompilation: no
Title: RPPA datasets from The Cancer Genome Atlas Project
Description: Package provides RPPA datasets from The Cancer Genome
Atlas Project for all available cohorts types from
http://gdac.broadinstitute.org/. Data format is explained here
https://wiki.nci.nih.gov/display/TCGA/Protein+Array
+Data+Format+Specification?src=search
biocViews: AnnotationData
Author: Witold Chodor <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.RPPA
git_branch: RELEASE_3_21
git_last_commit: a0e9a42
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RTCGA.RPPA_1.36.0.tar.gz
vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html
vignetteTitles: Using RTCGA to download RPPA data as included in
RTCGA.RPPA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R
suggestsMe: RTCGA
dependencyCount: 130
Package: RUVnormalizeData
Version: 1.28.0
Depends: R (>= 2.10.0), Biobase
License: GPL-3
MD5sum: 324f0f2be61d1098a83c065bf97f21e7
NeedsCompilation: no
Title: Gender data for the RUVnormalize package
Description: Microarray gene expression data from the study of Vawter
et al., 2004.
biocViews: MicroarrayData
Author: Laurent Jacob
Maintainer: Laurent Jacob <laurent.jacob@univ-lyon1.fr>
git_url: https://git.bioconductor.org/packages/RUVnormalizeData
git_branch: RELEASE_3_21
git_last_commit: c880da1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/RUVnormalizeData_1.28.0.tar.gz
vignettes: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.pdf
vignetteTitles: RUVnormalizeData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.R
importsMe: RUVnormalize
dependencyCount: 7
Package: sampleClassifierData
Version: 1.32.0
Depends: R (>= 3.5.0), SummarizedExperiment
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 660286587c32a7683576819525dde6a2
NeedsCompilation: no
Title: Pre-processed data for use with the sampleClassifier package
Description: This package contains two microarray and two RNA-seq
datasets that have been preprocessed for use with the
sampleClassifier package. The RNA-seq data are derived from
Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The
microarray data are derived from Roth et al. (2006) and Ge et
al. (2005).
biocViews: ExperimentData, ExpressionData, MicroarrayData,
SequencingData, RNASeqData, ArrayExpress
Author: Khadija El Amrani
Maintainer: Khadija El Amrani <khadija.el-amrani@charite.de>
git_url: https://git.bioconductor.org/packages/sampleClassifierData
git_branch: RELEASE_3_21
git_last_commit: d2d5aad
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/sampleClassifierData_1.32.0.tar.gz
vignettes:
vignettes/sampleClassifierData/inst/doc/sampleClassifierData.pdf
vignetteTitles: sampleClassifierData Introduction
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.R
suggestsMe: sampleClassifier
dependencyCount: 36
Package: SBGNview.data
Version: 1.22.0
Depends: R (>= 3.6)
Imports: knitr, rmarkdown, bookdown
Suggests: SummarizedExperiment
License: AGPL-3
MD5sum: c93783958c0aeee489db2d990f923146
NeedsCompilation: no
Title: Supporting datasets for SBGNview package
Description: This package contains: 1. A microarray gene expression
dataset from a human breast cancer study. 2. A RNA-Seq gene
expression dataset from a mouse study on IFNG knockout. 3. ID
mapping tables between gene IDs and SBGN-ML file glyph IDs. 4.
Percent of orthologs detected in other species of the genes in
a pathway. Cutoffs of this percentage for defining if a pathway
exists in another species. 5. XML text of SBGN-ML files for all
pre-collected pathways.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, GEO, RNASeqData
Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo
Maintainer: Weijun Luo <luo_weijun@yahoo.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SBGNview.data
git_branch: RELEASE_3_21
git_last_commit: 3bea9d8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SBGNview.data_1.22.0.tar.gz
vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html
vignetteTitles: Supporting Datasets for SBGNview Package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R
dependsOnMe: SBGNview
dependencyCount: 32
Package: scaeData
Version: 1.4.0
Depends: R (>= 4.4.0)
Imports: ExperimentHub
Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment,
Matrix, BiocStyle
License: MIT + file LICENSE
MD5sum: 3e8528d2789b0b0c3f7df62b8db4d785
NeedsCompilation: no
Title: Data Package for SingleCellAlleleExperiment
Description: Contains default datasets used by the Bioconductor package
SingleCellAlleleExperiment. The raw FASTQ files were sourced
from publicly accessible datasets provided by 10x Genomics.
Subsequently, our scIGD snakemake workflow was employed to
process these FASTQ files. The resulting output from scIGD
constitutes to the contents of this data package.
biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data,
SingleCellData
Author: Ahmad Al Ajami [aut, cre] (ORCID:
<https://orcid.org/0009-0006-5615-7447>), Jonas Schuck [aut]
(ORCID: <https://orcid.org/0009-0003-5705-4579>), Federico
Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>),
Katharina Imkeller [aut] (ORCID:
<https://orcid.org/0000-0002-5177-0852>)
Maintainer: Ahmad Al Ajami <alajami@med.uni-frankfurt.de>
URL: https://github.com/AGImkeller/scaeData
VignetteBuilder: knitr
BugReports: https://github.com/AGImkeller/scIGD/issues
git_url: https://git.bioconductor.org/packages/scaeData
git_branch: RELEASE_3_21
git_last_commit: 976e2af
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scaeData_1.4.0.tar.gz
vignettes: vignettes/scaeData/inst/doc/scaeData.html
vignetteTitles: scaeData User Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/scaeData/inst/doc/scaeData.R
suggestsMe: SingleCellAlleleExperiment
dependencyCount: 65
Package: scanMiRData
Version: 1.14.0
Depends: R (>= 4.0)
Imports: scanMiR, utils
Suggests: knitr, rmarkdown, BiocStyle
License: GPL-3
MD5sum: 45fec97eac7c55d13fbb637f9fa68adb
NeedsCompilation: no
Title: miRNA Affinity models for the scanMiR package
Description: This package contains companion data to the scanMiR
package. It contains `KdModel` (miRNA 12-mer binding affinity
models) collections corresponding to all human, mouse and rat
mirbase miRNAs. See the scanMiR package for details.
biocViews: miRNAData, ExperimentData, Homo_sapiens_Data,
Mus_musculus_Data, Rattus_norvegicus_Data
Author: Pierre-Luc Germain [cre, aut] (ORCID:
<https://orcid.org/0000-0003-3418-4218>), Michael Soutschek
[aut], Fridolin Gross [aut]
Maintainer: Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scanMiRData
git_branch: RELEASE_3_21
git_last_commit: e9b652f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scanMiRData_1.14.0.tar.gz
vignettes: vignettes/scanMiRData/inst/doc/scanMiRData.html
vignetteTitles: scanMiRData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scanMiRData/inst/doc/scanMiRData.R
importsMe: scanMiRApp
dependencyCount: 68
Package: scATAC.Explorer
Version: 1.14.0
Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors, zellkonverter
Imports: methods, Matrix
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
License: Artistic-2.0
MD5sum: 7a2c2a4b971b2f82989b884beba5b78c
NeedsCompilation: no
Title: A Collection of Single-cell ATAC Sequencing Datasets and
Corresponding Metadata
Description: This package provides a tool to search and download a
collection of publicly available single cell ATAC-seq datasets
and their metadata. scATAC-Explorer aims to act as a single
point of entry for users looking to study single cell ATAC-seq
data. Users can quickly search available datasets using the
metadata table and download datasets of interest for immediate
analysis within R.
biocViews: SingleCellData, SequencingData, ExpressionData, GEO, Tissue,
Genome, PackageTypeData
Author: Arrian Gibson-Khademi [aut, cre], Erik Christensen [aut],
Jonathan Wang [aut], Parisa Shooshtari [aut]
Maintainer: Arrian Gibson-Khademi <agibsonk@uwo.ca>
VignetteBuilder: knitr
BugReports: https://github.com/shooshtarilab/scATACseq/issues
git_url: https://git.bioconductor.org/packages/scATAC.Explorer
git_branch: RELEASE_3_21
git_last_commit: 0812e0a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scATAC.Explorer_1.14.0.tar.gz
vignettes: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.html
vignetteTitles: scATAC.Explorer
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.R
dependencyCount: 80
Package: SCLCBam
Version: 1.40.0
Depends: R(>= 2.10)
Suggests: BiocStyle
License: GPL-2
MD5sum: 9668d4f60766853b7d636aa8986b107c
NeedsCompilation: no
Title: Sequence data from chromosome 4 of a small-cell lung tumor
Description: Whole-exome sequencing data from a murine small-cell lung
tumor; only contains data of chromosome 4.
biocViews: SequencingData, LungCancerData
Author: Thomas Kuilman
Maintainer: Oscar Krijgsman <o.krijgsman@nki.nl>
git_url: https://git.bioconductor.org/packages/SCLCBam
git_branch: RELEASE_3_21
git_last_commit: 465c2ab
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SCLCBam_1.40.0.tar.gz
vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf
vignetteTitles: SCLCBam
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R
dependencyCount: 0
Package: scMultiome
Version: 1.8.0
Depends: AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment,
SingleCellExperiment, SummarizedExperiment
Imports: AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate,
methods, rhdf5, alabaster.matrix
Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi,
testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
License: CC BY-SA 4.0
MD5sum: 969211ca6f411e2104c8d5508dc7cc48
NeedsCompilation: no
Title: Collection of Public Single-Cell Multiome (scATAC + scRNAseq)
Datasets
Description: Single cell multiome data, containing chromatin
accessibility (scATAC-seq) and gene expression (scRNA-seq)
information analyzed with the ArchR package and presented as
MultiAssayExperiment objects.
biocViews: PackageTypeData, ExperimentHub, SingleCellData,
ExpressionData, SequencingData, Homo_sapiens_Data, CellCulture,
Tissue, GEO
Author: Xiaosai Yao [cre, aut] (ORCID:
<https://orcid.org/0000-0001-9729-0726>), Aleksander Chlebowski
[aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz WÅ‚odarczyk
[aut]
Maintainer: Xiaosai Yao <xiaosai.yao@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scMultiome
git_branch: RELEASE_3_21
git_last_commit: 5963978
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scMultiome_1.8.0.tar.gz
vignettes: vignettes/scMultiome/inst/doc/scMultiome.html
vignetteTitles: scMultiome tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scMultiome/inst/doc/scMultiome.R
importsMe: epiregulon
suggestsMe: epiregulon.extra
dependencyCount: 101
Package: scpdata
Version: 1.16.1
Depends: R (>= 4.2.0), QFeatures, ExperimentHub
Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors
Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown,
testthat
License: GPL-2
MD5sum: 50a9767c61dde19ddff4288a02452c6f
NeedsCompilation: no
Title: Single-Cell Proteomics Data Package
Description: The package disseminates mass spectrometry (MS)-based
single-cell proteomics (SCP) datasets. The data were collected
from published work and formatted using the `scp` data
structure. The data sets contain quantitative information at
spectrum, peptide and/or protein level for single cells or
minute sample amounts.
biocViews: ExperimentData, ExpressionData, ExperimentHub,
ReproducibleResearch, MassSpectrometryData, Proteome,
SingleCellData, PackageTypeData
Author: Christophe Vanderaa [aut, cre] (ORCID:
<https://orcid.org/0000-0001-7443-5427>), Laurent Gatto [aut]
(ORCID: <https://orcid.org/0000-0002-1520-2268>), Enes Ayar
[dtc] (ORCID: <https://orcid.org/0000-0001-8881-9800>), Samuel
Grégoire [dtc] (ORCID: <https://orcid.org/0000-0002-0900-7677>)
Maintainer: Christophe Vanderaa <christophe.vanderaa@uclouvain.be>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scpdata
git_branch: RELEASE_3_21
git_last_commit: 229186a
git_last_commit_date: 2025-05-06
Date/Publication: 2025-05-08
source.ver: src/contrib/scpdata_1.16.1.tar.gz
vignettes: vignettes/scpdata/inst/doc/contribution_guidelines.html,
vignettes/scpdata/inst/doc/scpdata.html
vignetteTitles: Contribution guidelines, Data Package for Single Cell
Proteomics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scpdata/inst/doc/contribution_guidelines.R,
vignettes/scpdata/inst/doc/scpdata.R
suggestsMe: scp
dependencyCount: 122
Package: scRNAseq
Version: 2.22.0
Depends: SingleCellExperiment
Imports: utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray,
DelayedArray, GenomicRanges, SummarizedExperiment,
ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6),
AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base,
alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite
Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate,
BiocManager
License: CC0
MD5sum: 95cfbf6c65b77cea965926bacf8cc076
NeedsCompilation: no
Title: Collection of Public Single-Cell RNA-Seq Datasets
Description: Gene-level counts for a collection of public scRNA-seq
datasets, provided as SingleCellExperiment objects with cell-
and gene-level metadata.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData, SingleCellData
Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb,
cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte
Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb],
Milan Malfait [ctb]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: RELEASE_3_21
git_last_commit: 62a2b70
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scRNAseq_2.22.0.tar.gz
vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html
vignetteTitles: User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R
dependsOnMe: OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.workflows,
SingleRBook
importsMe: singleCellTK
suggestsMe: APL, BASiCS, batchelor, bluster, ccImpute,
ClusterFoldSimilarity, destiny, dittoSeq, Glimma, iSEE,
iSEEfier, iSEEhex, iSEEindex, iSEEu, miloR, miQC, mumosa,
ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics,
scDotPlot, scFeatureFilter, scone, scran, scrapper, scTreeViz,
scuttle, SingleCellExperiment, SingleR, SplineDV, UCell,
velociraptor, zellkonverter, zinbwave, scStability, speakeasyR
dependencyCount: 118
Package: scTHI.data
Version: 1.20.0
Depends: R (>= 4.0)
License: GPL-2
MD5sum: 1e048e6bcd938bff3ba6ee6a92a1d2b7
NeedsCompilation: no
Title: The package contains examples of single cell data used in
vignettes and examples of the scTHI package; data contain both
tumor cells and immune cells from public dataset of glioma
Description: Data for the vignette and tutorial of the package scTHI.
biocViews: ExperimentData, SingleCellData
Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre]
Maintainer: Michele Ceccarelli <m.ceccarelli@gmail.com>
git_url: https://git.bioconductor.org/packages/scTHI.data
git_branch: RELEASE_3_21
git_last_commit: 9e16ff0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/scTHI.data_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: scTHI
dependencyCount: 0
Package: seq2pathway.data
Version: 1.40.0
Depends: R (>= 3.6.2)
License: GPL (>= 2)
MD5sum: 7a78db6fa35357ab7f148785eafee6bb
NeedsCompilation: no
Title: data set for R package seq2pathway
Description: Supporting data for the seq2patheway package. Includes
modified gene sets from MsigDB and org.Hs.eg.db; gene locus
definitions from GENCODE project.
biocViews: ExperimentData
Author: Bin Wang <binw@uchicago.edu>
Maintainer: Arjun Kinstlick <akinstlick@uchicago.edu>
git_url: https://git.bioconductor.org/packages/seq2pathway.data
git_branch: RELEASE_3_21
git_last_commit: b0a8b53
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/seq2pathway.data_1.40.0.tar.gz
vignettes: vignettes/seq2pathway.data/inst/doc/seq2pathway.data.pdf
vignetteTitles: An R data package for sequence
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: seq2pathway
dependencyCount: 0
Package: seqc
Version: 1.42.0
Depends: R (>= 2.10)
Imports: utils, Biobase
License: GPL-3
MD5sum: a11df082c73cda19addfcd462530c898
NeedsCompilation: no
Title: RNA-seq data generated from SEQC (MAQC-III) study
Description: The SEQC/MAQC-III Consortium has produced benchmark
RNA-seq data for the assessment of RNA sequencing technologies
and data analysis methods (Nat Biotechnol, 2014). Billions of
sequence reads have been generated from ten different
sequencing sites. This package contains the summarized read
count data for ~2000 sequencing libraries. It also includes all
the exon-exon junctions discovered from the study. TaqMan
RT-PCR data for ~1000 genes and ERCC spike-in sequence data are
included in this package as well.
biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData
Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth
and Steve Lianoglou.
Maintainer: Yang Liao <Yang.Liao@onjcri.org.au> and Wei Shi
<Wei.Shi@onjcri.org.au>
URL:
http://bioconductor.org/packages/release/data/experiment/html/seqc.html
git_url: https://git.bioconductor.org/packages/seqc
git_branch: RELEASE_3_21
git_last_commit: 9507cc9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/seqc_1.42.0.tar.gz
vignettes: vignettes/seqc/inst/doc/seqc.pdf
vignetteTitles: SEQC Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/seqc/inst/doc/seqc.R
dependencyCount: 7
Package: serumStimulation
Version: 1.44.0
Depends: R (>= 2.10)
License: GPL (>= 2)
MD5sum: 5a7a96fc68deb4d6874e2f403a989a3b
NeedsCompilation: no
Title: serumStimulation is a data package which is used by examples in
package pcaGoPromoter
Description: Contains 13 micro array data results from a serum
stimulation experiment
biocViews: ExperimentData, MicroarrayData
Author: Morten Hansen <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
git_url: https://git.bioconductor.org/packages/serumStimulation
git_branch: RELEASE_3_21
git_last_commit: df629e2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/serumStimulation_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: sesameData
Version: 1.26.0
Depends: R (>= 4.2.0), ExperimentHub, AnnotationHub
Imports: utils, readr, stringr, GenomicRanges, S4Vectors, IRanges,
GenomeInfoDb
Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown
License: Artistic-2.0
MD5sum: bea93b6a145d6235e3afa8e031180e54
NeedsCompilation: no
Title: Supporting Data for SeSAMe Package
Description: Provides supporting annotation and test data for SeSAMe
package. This includes chip tango addresses, mapping
information, performance annotation, and trained predictor for
Infinium array data. This package provides user access to
essential annotation data for working with many generations of
the Infinium DNA methylation array. Current we support human
array (HM27, HM450, EPIC), mouse array (MM285) and the
HorvathMethylChip40 (Mammal40) array.
biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub,
MethylationArrayData
Author: Wanding Zhou [aut, cre] (ORCID:
<https://orcid.org/0000-0001-9126-1932>), Hui Shen [aut],
Timothy Triche [ctb]
Maintainer: Wanding Zhou <zhouwanding@gmail.com>
URL: https://github.com/zwdzwd/sesame
VignetteBuilder: knitr
BugReports: https://github.com/zwdzwd/sesame/issue
git_url: https://git.bioconductor.org/packages/sesameData
git_branch: RELEASE_3_21
git_last_commit: e4c750c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/sesameData_1.26.0.tar.gz
vignettes: vignettes/sesameData/inst/doc/sesameData.html
vignetteTitles: sesameData User Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sesameData/inst/doc/sesameData.R
dependsOnMe: sesame
importsMe: knowYourCG, MethReg, TENET, CytoMethIC
suggestsMe: ELMER, iNETgrate
dependencyCount: 73
Package: seventyGeneData
Version: 1.44.0
Depends: R (>= 2.13.0)
Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl,
BiocStyle
License: Artistic-2.0
MD5sum: 985a6f7066d4b87809b3bb8d5e8c1695
NeedsCompilation: no
Title: ExpressionSets from the van't Veer and Van de Vijver breast
cancer studies
Description: Gene expression data for the two breast cancer cohorts
published by van't Veer and Van de Vijver in 2002.
biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData
Author: Luigi Marchionni [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7336-8071>), Claudio Zanettini
[aut, ctb], Lucio Queiroz [aut, ctb] (ORCID:
<https://orcid.org/0000-0002-6090-1834>)
Maintainer: Luigi Marchionni <lum403@med.cornell.edu>
URL:
https://bioconductor.org/packages/release/data/experiment/html/seventyGeneData.html
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/seventyGeneData
git_branch: RELEASE_3_21
git_last_commit: b5bc0ba
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/seventyGeneData_1.44.0.tar.gz
vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.html
vignetteTitles: 1. Working with the seventyGeneData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R
dependencyCount: 0
Package: SFEData
Version: 1.10.0
Depends: R (>= 4.1.0)
Imports: BiocFileCache, AnnotationHub, ExperimentHub, utils
Suggests: BiocStyle, knitr, rmarkdown, SeuratObject,
SpatialFeatureExperiment, testthat (>= 3.0.0)
License: Artistic-2.0
MD5sum: 119748229825579a8f05ce7391cc428d
NeedsCompilation: no
Title: Example SpatialFeatureExperiment datasets
Description: Example spatial transcriptomics datasets with Simple
Feature annotations as SpatialFeatureExperiment objects.
Technologies include Visium, slide-seq, Nanostring CoxMX,
Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal
muscle, human melanoma metastasis, human lung, breast cancer,
and mouse liver.
biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data,
Homo_sapiens_Data, SpatialData, Tissue, SingleCellData
Author: Lambda Moses [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7092-9427>), Alik Huseynov [aut]
(ORCID: <https://orcid.org/0000-0002-1438-4389>), Kayla Jackson
[aut] (ORCID: <https://orcid.org/0000-0001-6483-0108>), Lior
Pachter [aut, ths] (ORCID:
<https://orcid.org/0000-0002-9164-6231>)
Maintainer: Lambda Moses <dlu2@caltech.edu>
URL: https://github.com/pachterlab/SFEData
VignetteBuilder: knitr
BugReports: https://github.com/pachterlab/SFEData/issues
git_url: https://git.bioconductor.org/packages/SFEData
git_branch: RELEASE_3_21
git_last_commit: dab441b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SFEData_1.10.0.tar.gz
vignettes: vignettes/SFEData/inst/doc/SFEData.html
vignetteTitles: Example SpatialFeatureExperiment datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SFEData/inst/doc/SFEData.R
suggestsMe: alabaster.sfe, concordexR, jazzPanda,
SpatialFeatureExperiment, Voyager, xenLite
dependencyCount: 65
Package: shinyMethylData
Version: 1.28.0
Depends: R (>= 3.0.0)
License: Artistic-2.0
MD5sum: 8516878331cfd6b78744f700426d3866
NeedsCompilation: no
Title: Example dataset of input data for shinyMethyl
Description: Extracted data from 369 TCGA Head and Neck Cancer DNA
methylation samples. The extracted data serve as an example
dataset for the package shinyMethyl. Original samples are from
450k methylation arrays, and were obtained from The Cancer
Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched
normals and 9 are technical replicates of a control cell line.
biocViews: Genome, CancerData
Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut]
Maintainer: Jean-Philippe Fortin <jfortin@jhsph.edu>
git_url: https://git.bioconductor.org/packages/shinyMethylData
git_branch: RELEASE_3_21
git_last_commit: c70f362
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/shinyMethylData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: shinyMethyl
dependencyCount: 0
Package: signatureSearchData
Version: 1.22.0
Depends: R (>= 3.6)
Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, rhdf5
Suggests: knitr, rmarkdown
License: Artistic-2.0
MD5sum: cb9c051bffd7b718ed54cc96ae68e2ca
NeedsCompilation: no
Title: Datasets for signatureSearch package
Description: CMAP/LINCS hdf5 databases and other annotations used for
signatureSearch software package.
biocViews: ExperimentHub, ExperimentData, ExpressionData
Author: Yuzhu Duan <yduan004@ucr.edu>, Brendan Gongol
<bgong001@ucr.edu>, Thomas Girke <thomas.girke@ucr.edu>
Maintainer: Brendan Gongol <bgong001@ucr.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/signatureSearchData
git_branch: RELEASE_3_21
git_last_commit: 79c1dd9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/signatureSearchData_1.22.0.tar.gz
vignettes:
vignettes/signatureSearchData/inst/doc/signatureSearchData.html
vignetteTitles: signatureSearchData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R
dependsOnMe: DFD
suggestsMe: signatureSearch
dependencyCount: 76
Package: SimBenchData
Version: 1.16.0
Depends: ExperimentHub
Imports: S4Vectors, utils
Suggests: BiocStyle, knitr, rmarkdown, Seurat
License: GPL-3
MD5sum: cdb763c19b5ae1bb8b2a867f25033687
NeedsCompilation: no
Title: SimBenchData: a collection of 35 single-cell RNA-seq data
covering a wide range of data characteristics
Description: The SimBenchData package contains a total of 35
single-cell RNA-seq datasets covering a wide range of data
characteristics, including major sequencing protocols, multiple
tissue types, and both human and mouse sources.
biocViews: ExperimentHub, ExperimentData, SingleCellData, RNASeqData,
Tissue, SequencingData
Author: Yue Cao [aut, cre], Pengyi Yang [aut], Jean Yee Hwa Yang [aut]
Maintainer: Yue Cao <ycao6928@uni.sydney.edu.au>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SimBenchData
git_branch: RELEASE_3_21
git_last_commit: 9961930
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SimBenchData_1.16.0.tar.gz
vignettes: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.html
vignetteTitles: SimBenchData: a collection of single-cell RNA-seq data
covering a wide range of data characteristics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.R
dependencyCount: 65
Package: simpIntLists
Version: 1.44.0
License: GPL (>= 2)
MD5sum: cbfb771fafc6a47521736aec605b55e4
NeedsCompilation: no
Title: The package contains BioGRID interactions for various organisms
in a simple format
Description: The package contains BioGRID interactions for
arabidopsis(thale cress), c.elegans, fruit fly, human, mouse,
yeast( budding yeast ) and S.pombe (fission yeast) . Entrez
ids, official names and unique ids can be used to find
proteins. The format of interactions are lists. For each
gene/protein, there is an entry in the list with "name"
containing name of the gene/protein and "interactors"
containing the list of genes/proteins interacting with it.
biocViews: ExperimentData, Arabidopsis_thaliana_Data
Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay
Maintainer: Kircicegi Korkmaz <e102771@ceng.metu.edu.tr>
git_url: https://git.bioconductor.org/packages/simpIntLists
git_branch: RELEASE_3_21
git_last_commit: 85940a5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/simpIntLists_1.44.0.tar.gz
vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf
vignetteTitles: simpIntLists
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R
dependsOnMe: ibh
dependencyCount: 0
Package: Single.mTEC.Transcriptomes
Version: 1.36.0
Depends: R (>= 3.5.0)
Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr, BiocParallel
License: LGPL
MD5sum: d064909489353a3692d4035066149a83
NeedsCompilation: no
Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells
Description: This data package contains the code used to analyse the
single-cell RNA-seq and the bulk ATAC-seq data from the
manuscript titled: Single-cell transcriptome analysis reveals
coordinated ectopic-gene expression patterns in medullary
thymic epithelial cells. This paper was published in Nature
Immunology 16,933-941(2015). The data objects provided in this
package has been pre-processed: the raw data files can be
downloaded from ArrayExpress under the accession identifiers
E-MTAB-3346 and E-MTAB-3624. The vignette of this data package
provides a documented and reproducible workflow that includes
the code that was used to generate each statistic and figure
from the manuscript.
biocViews: ExperimentData
Author: Alejandro Reyes
Maintainer: Alejandro Reyes <alejandro.reyes.ds@gmail.com>
VignetteBuilder: knitr
git_url:
https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes
git_branch: RELEASE_3_21
git_last_commit: a8ea387
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/Single.mTEC.Transcriptomes_1.36.0.tar.gz
vignettes: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.pdf
vignetteTitles: Analysis of single cell mTEC data.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.R
dependencyCount: 0
Package: SingleCellMultiModal
Version: 1.20.0
Depends: R (>= 4.2.0), MultiAssayExperiment
Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub,
graphics, HDF5Array, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown,
scater, scran, UpSetR, uwot
License: Artistic-2.0
MD5sum: f596ef12d970820fc14c37a656f86ab8
NeedsCompilation: no
Title: Integrating Multi-modal Single Cell Experiment datasets
Description: SingleCellMultiModal is an ExperimentHub package that
serves multiple datasets obtained from GEO and other sources
and represents them as MultiAssayExperiment objects. We provide
several multi-modal datasets including scNMT, 10X Multiome,
seqFISH, CITEseq, SCoPE2, and others. The scope of the package
is is to provide data for benchmarking and analysis. To cite,
use the 'citation' function and see
<https://doi.org/10.1371/journal.pcbi.1011324>.
biocViews: ExperimentData, SingleCellData, ReproducibleResearch,
ExperimentHub, GEO
Author: Marcel Ramos [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3242-0582>), Ricard Argelaguet
[aut], Al Abadi [ctb], Dario Righelli [aut], Christophe
Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger
[aut], Levi Waldron [aut]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues
git_url: https://git.bioconductor.org/packages/SingleCellMultiModal
git_branch: RELEASE_3_21
git_last_commit: 32afbd3
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SingleCellMultiModal_1.20.0.tar.gz
vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html,
vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html,
vignettes/SingleCellMultiModal/inst/doc/GTseq.html,
vignettes/SingleCellMultiModal/inst/doc/scMultiome.html,
vignettes/SingleCellMultiModal/inst/doc/scNMT.html,
vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html,
vignettes/SingleCellMultiModal/inst/doc/seqFISH.html,
vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.html
vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, GT-seq
Mouse Embryo, scMultiome 10x PBMC, scNMT Mouse Gastrulation,
SCoPE2: macrophage vs monocytes, seqFISH Mouse Visual Cortex,
SingleCellMultiModal Introduction
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SingleCellMultiModal/inst/doc/CITEseq.R,
vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.R,
vignettes/SingleCellMultiModal/inst/doc/GTseq.R,
vignettes/SingleCellMultiModal/inst/doc/scMultiome.R,
vignettes/SingleCellMultiModal/inst/doc/scNMT.R,
vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R,
vignettes/SingleCellMultiModal/inst/doc/seqFISH.R,
vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.R
suggestsMe: decontX, MuData, StabMap
dependencyCount: 88
Package: SingleMoleculeFootprintingData
Version: 1.16.0
Imports: ExperimentHub, utils
Suggests: knitr, rmarkdown
License: GPL-3
MD5sum: e13f1b3126441c183a1004e7b4c2bcc3
NeedsCompilation: no
Title: Data supporting the SingleMoleculeFootprinting pkg
Description: This Data package contains data objcets relevanat for the
SingleMoleculeFootprinting package. More specifically, it
contains one example of aligned sequencing data (.bam & .bai)
necessary to run the SingleMoleculeFootprinting vignette.
Additionally, we provide data that are essential for some
functions to work correctly such as BaitCapture() and
SampleCorrelation().
biocViews: ExperimentHub, ExperimentData, SequencingData
Author: Guido Barzaghi [aut, cre] (ORCID:
<https://orcid.org/0000-0001-6066-3920>), Arnaud Krebs [aut]
(ORCID: <https://orcid.org/0000-0001-7999-6127>), Mike Smith
[ctb] (ORCID: <https://orcid.org/0000-0002-7800-3848>)
Maintainer: Guido Barzaghi <guido.barzaghi@embl.de>
VignetteBuilder: knitr
git_url:
https://git.bioconductor.org/packages/SingleMoleculeFootprintingData
git_branch: RELEASE_3_21
git_last_commit: 8409153
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SingleMoleculeFootprintingData_1.16.0.tar.gz
vignettes:
vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.html
vignetteTitles: SingleMoleculeFootprintingData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles:
vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.R
suggestsMe: SingleMoleculeFootprinting
dependencyCount: 65
Package: smokingMouse
Version: 1.6.0
Suggests: AnnotationHubData, BiocStyle, ExperimentHub,
ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0)
License: Artistic-2.0
MD5sum: 122c1f366e83fb1bd5aa0d95b10080eb
NeedsCompilation: no
Title: Provides access to smokingMouse project data
Description: This is an ExperimentHub package that provides access to
the data generated and analyzed in the
[smoking-nicotine-mouse](https://github.com/LieberInstitute/smoking-nicotine-mouse/)
LIBD project. The datasets contain the expression data of mouse
genes, transcripts, exons, and exon-exon junctions across 208
samples from pup and adult mouse brain, and adult blood, that
were exposed to nicotine, cigarette smoke, or controls. They
also contain relevant metadata of these samples and gene
expression features, such QC metrics, if they were used after
filtering steps and also if the features were differently
expressed in the different experiments.
biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, RNASeqData
Author: Daianna Gonzalez-Padilla [aut, cre] (ORCID:
<https://orcid.org/0009-0005-8348-3195>)
Maintainer: Daianna Gonzalez-Padilla <glezdaianna@gmail.com>
URL: https://github.com/LieberInstitute/smokingMouse
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/tag/smokingMouse
git_url: https://git.bioconductor.org/packages/smokingMouse
git_branch: RELEASE_3_21
git_last_commit: ca897b9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/smokingMouse_1.6.0.tar.gz
vignettes: vignettes/smokingMouse/inst/doc/smokingMouse.html
vignetteTitles: Introduction to smokingMouse
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/smokingMouse/inst/doc/smokingMouse.R
dependencyCount: 0
Package: SNAData
Version: 1.54.0
Depends: R (>= 2.4.0), graph
Suggests: Rgraphviz
License: LGPL
MD5sum: 5f5e9312259fb7f09fca216dcb013b1c
NeedsCompilation: no
Title: Social Networks Analysis Data Examples
Description: Data from Wasserman & Faust (1999) "Social Network
Analysis"
biocViews: ExperimentData
Author: Denise Scholtens
Maintainer: Denise Scholtens <dscholtens@northwestern.edu>
git_url: https://git.bioconductor.org/packages/SNAData
git_branch: RELEASE_3_21
git_last_commit: 42d9de1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SNAData_1.54.0.tar.gz
vignettes: vignettes/SNAData/inst/doc/SNAData.pdf
vignetteTitles: SNAData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SNAData/inst/doc/SNAData.R
dependencyCount: 8
Package: SNAGEEdata
Version: 1.44.0
Depends: R (>= 2.6.0)
Suggests: ALL, hgu95av2.db, SNAGEE
License: Artistic-2.0
MD5sum: 9f637e300886e8ee06cc66d09d55ab75
NeedsCompilation: no
Title: SNAGEE data
Description: SNAGEE data - gene list and correlation matrix
biocViews: MicroarrayData
Author: David Venet <davenet@ulb.ac.be>
Maintainer: David Venet <davenet@ulb.ac.be>
URL: http://fleming.ulb.ac.be/SNAGEE
git_url: https://git.bioconductor.org/packages/SNAGEEdata
git_branch: RELEASE_3_21
git_last_commit: 27e11a7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SNAGEEdata_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: SNAGEE
dependencyCount: 0
Package: SNPhoodData
Version: 1.38.0
Depends: R (>= 3.2)
Suggests: BiocStyle,knitr,rmarkdown
License: LGPL (>= 3)
MD5sum: 283628edd0818a21fb1f12b7ef222050
NeedsCompilation: no
Title: Additional and more complex example data for the SNPhood package
Description: This companion package for SNPhood provides some example
datasets of a larger size than allowed for the SNPhood package.
They include full and real-world examples for performing
analyses with the SNPhood package.
biocViews: ExperimentData
Author: Christian Arnold, Judith Zaugg
Maintainer: Christian Arnold <christian.arnold@embl.de>
VignetteBuilder: knitr
BugReports: christian.arnold@embl.de
git_url: https://git.bioconductor.org/packages/SNPhoodData
git_branch: RELEASE_3_21
git_last_commit: 14607c2
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SNPhoodData_1.38.0.tar.gz
vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html
vignetteTitles: The *SNPhoodData* package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: SNPhood
dependencyCount: 0
Package: SomatiCAData
Version: 1.46.0
Depends: R (>= 2.14)
License: Artistic-2.0
MD5sum: 3a702f22610d2efb7954bd27f65e4c05
NeedsCompilation: no
Title: An example cancer whole genome sequencing data for the SomatiCA
package
Description: An example cancer whole genome sequencing data for the
SomatiCA package
biocViews: ExperimentData, Genome, CancerData, SequencingData
Author: Mengjie Chen
Maintainer: Mengjie Chen <mengjie.chen@yale.edu>
git_url: https://git.bioconductor.org/packages/SomatiCAData
git_branch: RELEASE_3_21
git_last_commit: 0af5e9f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SomatiCAData_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: SomaticCancerAlterations
Version: 1.44.0
Depends: R (>= 3.5.0)
Imports: GenomicRanges, IRanges, S4Vectors
Suggests: testthat, ggbio, ggplot2, knitr
License: GPL-3
MD5sum: 438d272de78ab367acddc453c31f31af
NeedsCompilation: no
Title: Somatic Cancer Alterations
Description: Collection of somatic cancer alteration datasets
biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI
Author: Julian Gehring
Maintainer: Julian Gehring <jg-bioc@gmx.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations
git_branch: RELEASE_3_21
git_last_commit: 4c474da
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SomaticCancerAlterations_1.44.0.tar.gz
vignettes:
vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html
vignetteTitles: SomaticCancerAlterations - HTML
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R
suggestsMe: SomaticSignatures
dependencyCount: 23
Package: SpatialDatasets
Version: 1.6.3
Depends: ExperimentHub, SpatialExperiment,
Imports: utils
Suggests: BiocStyle, knitr, rmarkdown, cytomapper
License: GPL-3
MD5sum: e0cd4a3fcb264a7e907eaea67eb62c76
NeedsCompilation: no
Title: Collection of spatial omics datasets
Description: This is a collection of publically available spatial omics
datasets. Where possible we have curated these datasets as
either SpatialExperiments, MoleculeExperiments or
CytoImageLists and included annotations of the sample
characteristics.
biocViews: ExperimentData, ExperimentHub, ReproducibleResearch,
SingleCellData, SpatialData, Homo_sapiens_Data,
Mus_musculus_Data
Author: Farhan Ameen [aut], Nick Robertson [aut], Alex Qin [aut],
Shreya Rao [aut], Elijah Willie [aut], Ellis Patrick [aut, cre]
Maintainer: Ellis Patrick <ellis.patrick@sydney.edu.au>
URL: https://github.com/SydneyBioX/SpatialDatasets
VignetteBuilder: knitr
BugReports: https://github.com/SydneyBioX/SpatialDatasets/issues
git_url: https://git.bioconductor.org/packages/SpatialDatasets
git_branch: RELEASE_3_21
git_last_commit: ea2889c
git_last_commit_date: 2025-05-20
Date/Publication: 2025-05-22
source.ver: src/contrib/SpatialDatasets_1.6.3.tar.gz
vignettes:
vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.html
vignetteTitles: The SpatialDataset package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.R
suggestsMe: lisaClust, spicyR, spicyWorkflow
dependencyCount: 81
Package: spatialDmelxsim
Version: 1.14.0
Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment
Imports: utils
Suggests: knitr, rmarkdown, BiocStyle
License: GPL-3
MD5sum: 41f6a5537919134e6bd7c10bbf129ad0
NeedsCompilation: no
Title: Spatial allelic expression counts for fly cross embryo
Description: Spatial allelic expression counts from Combs & Fraser
(2018), compiled into a SummarizedExperiment object. This
package contains data of allelic expression counts of spatial
slices of a fly embryo, a Drosophila melanogaster x Drosophila
simulans cross. See the CITATION file for the data source, and
the associated script for how the object was constructed from
publicly available data.
biocViews: ExperimentHub, SequencingData, RNASeqData, ExpressionData,
Drosophila_melanogaster_Data, GEO
Author: Michael Love [aut, cre]
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
URL: https://github.com/mikelove/spatialDmelxsim
VignetteBuilder: knitr
BugReports: https://github.com/mikelove/spatialDmelxsim/issues
git_url: https://git.bioconductor.org/packages/spatialDmelxsim
git_branch: RELEASE_3_21
git_last_commit: 381ea05
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/spatialDmelxsim_1.14.0.tar.gz
vignettes: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.html
vignetteTitles: spatialDmelxsim
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.R
dependencyCount: 76
Package: spatialLIBD
Version: 1.20.1
Depends: R (>= 4.1.0), SpatialExperiment (>= 1.3.3)
Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite,
shinyWidgets, sessioninfo, grid, grDevices, methods,
AnnotationHub, utils, png, scater, DT, ExperimentHub,
SummarizedExperiment, stats, graphics, S4Vectors, IRanges,
benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite,
tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges,
magick, paletteer, scuttle, edgeR, limma, statmod,
MatrixGenerics, rlang, dplyr, ComplexHeatmap, circlize
Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer
License: Artistic-2.0
MD5sum: b5f902c448b7d8330a9c1c3c51fcaebb
NeedsCompilation: no
Title: spatialLIBD: an R/Bioconductor package to visualize
spatially-resolved transcriptomics data
Description: Inspect interactively the spatially-resolved
transcriptomics data from the 10x Genomics Visium platform as
well as data from the Maynard, Collado-Torres et al, Nature
Neuroscience, 2021 project analyzed by Lieber Institute for
Brain Development (LIBD) researchers and collaborators.
biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData,
SingleCellData, ExpressionData, Tissue, PackageTypeData,
SpatialData
Author: Leonardo Collado-Torres [aut, cre] (ORCID:
<https://orcid.org/0000-0003-2140-308X>), Kristen R. Maynard
[ctb] (ORCID: <https://orcid.org/0000-0003-0031-8468>), Andrew
E. Jaffe [ctb] (ORCID:
<https://orcid.org/0000-0001-6886-1454>), Brenda Pardo [ctb]
(ORCID: <https://orcid.org/0000-0001-8103-7136>), Abby Spangler
[ctb] (ORCID: <https://orcid.org/0000-0002-0028-9348>), Jesús
Vélez Santiago [ctb] (ORCID:
<https://orcid.org/0000-0001-5128-3838>), Lukas M. Weber [ctb]
(ORCID: <https://orcid.org/0000-0002-3282-1730>), Louise
Huuki-Myers [ctb] (ORCID:
<https://orcid.org/0000-0001-5148-3602>), Nicholas Eagles [ctb]
(ORCID: <https://orcid.org/0000-0002-9808-5254>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
URL: https://github.com/LieberInstitute/spatialLIBD
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/tag/spatialLIBD
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_21
git_last_commit: 0537f4e
git_last_commit_date: 2025-04-30
Date/Publication: 2025-05-01
source.ver: src/contrib/spatialLIBD_1.20.1.tar.gz
vignettes:
vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html,
vignettes/spatialLIBD/inst/doc/multi_gene_plots.html,
vignettes/spatialLIBD/inst/doc/spatialLIBD.html,
vignettes/spatialLIBD/inst/doc/TenX_data_download.html
vignetteTitles: Guide to Spatial Registration, Guide to Multi-Gene
Plots, Introduction to spatialLIBD, Using spatialLIBD with 10x
Genomics public datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.R,
vignettes/spatialLIBD/inst/doc/multi_gene_plots.R,
vignettes/spatialLIBD/inst/doc/spatialLIBD.R,
vignettes/spatialLIBD/inst/doc/TenX_data_download.R
importsMe: DeconvoBuddies, visiumStitched
suggestsMe: Banksy, BatchSVG, BayesSpace, DESpace
dependencyCount: 199
Package: SpikeIn
Version: 1.50.0
Depends: R (>= 2.10), affy (>= 1.23.4)
License: Artistic-2.0
MD5sum: d12b9cbd74d9bcb17399e3bbc5f4fe4b
NeedsCompilation: no
Title: Affymetrix Spike-In Experiment Data
Description: Contains the HGU133 and HGU95 spikein experiment data.
biocViews: ExperimentData, MicroarrayData
Author: Rafael Irizarry <rafa@ds.dfci.harvard.edu>
Maintainer: Robert D Shear <rshear@ds.dfci.harvard.edu>
URL: https://bioconductor.org/packages/SpikeIn
BugReports: https://github.com/rafalab/SpikeIn/issues
git_url: https://git.bioconductor.org/packages/SpikeIn
git_branch: RELEASE_3_21
git_last_commit: 3d0c595
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SpikeIn_1.50.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PECA
dependencyCount: 12
Package: SpikeInSubset
Version: 1.48.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4)
License: LGPL
MD5sum: a174aee474447039636c2d49ad2390a4
NeedsCompilation: no
Title: Part of Affymetrix's Spike-In Experiment Data
Description: Includes probe-level and expression data for the HGU133
and HGU95 spike-in experiments
biocViews: ExperimentData, MicroarrayData
Author: Rafael Irizarry <rafa@ds.dfci.harvard.edu> and Zhijin Wu
Maintainer: Robert D Shear <rshear@ds.dfci.harvard.edu>
URL: https://bioconductor.org/packages/SpikeInSubset
BugReports: https://github.com/rafalab/SpikeInSubset/issues
git_url: https://git.bioconductor.org/packages/SpikeInSubset
git_branch: RELEASE_3_21
git_last_commit: 2413a3c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SpikeInSubset_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 12
Package: spqnData
Version: 1.20.0
Depends: R (>= 4.0), SummarizedExperiment
License: Artistic-2.0
MD5sum: 974e3426414f9d270deda774fac1b639
NeedsCompilation: no
Title: Data for the spqn package
Description: Bulk RNA-seq from GTEx on 4,000 randomly selected,
expressed genes. Data has been processed for co-expression
analysis.
biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData
Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut]
Maintainer: Yi Wang <yiwangthu5@gmail.com>
git_url: https://git.bioconductor.org/packages/spqnData
git_branch: RELEASE_3_21
git_last_commit: 8598ef6
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/spqnData_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: spqn
dependencyCount: 36
Package: stemHypoxia
Version: 1.44.0
Depends: R (>= 2.14.1)
License: GPL (>=2)
MD5sum: 35b3fb62d6fdaba14c962d91077f5610
NeedsCompilation: no
Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene
expression dataset by Prado-Lopez et al. (2010)
Description: Expression profiling using microarray technology to prove
if 'Hypoxia Promotes Efficient Differentiation of Human
Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez
et al. (2010) Stem Cells 28:407-418. Full data available at
Gene Expression Omnibus series GSE37761.
biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data,
CancerData, MicroarrayData, TissueMicroarrayData, GEO
Author: Cristobal Fresno and Elmer A. Fernandez
Maintainer: Cristobal Fresno <cristobalfresno@gmail.com>
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761,
http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract
git_url: https://git.bioconductor.org/packages/stemHypoxia
git_branch: RELEASE_3_21
git_last_commit: b95325d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/stemHypoxia_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: lmdme
dependencyCount: 0
Package: STexampleData
Version: 1.16.0
Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment
Imports: utils
Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array
License: MIT + file LICENSE
MD5sum: 39b818abecdab7281d945bfac960aa16
NeedsCompilation: no
Title: Collection of spatial transcriptomics datasets in
SpatialExperiment Bioconductor format
Description: Collection of spatial transcriptomics datasets stored in
SpatialExperiment Bioconductor format, for use in examples,
demonstrations, and tutorials. The datasets are from several
different platforms and have been sourced from various publicly
available sources. Several datasets include images and/or
reference annotation labels.
biocViews: ExperimentData, ExperimentHub, ReproducibleResearch,
ExpressionData, SingleCellData, SpatialData, Homo_sapiens_Data,
Mus_musculus_Data
Author: Lukas M. Weber [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3282-1730>), Yixing E. Dong [aut]
(ORCID: <https://orcid.org/0009-0003-5115-5686>)
Maintainer: Lukas M. Weber <lmweb012@gmail.com>
URL: https://github.com/lmweber/STexampleData
VignetteBuilder: knitr
BugReports: https://github.com/lmweber/STexampleData/issues
git_url: https://git.bioconductor.org/packages/STexampleData
git_branch: RELEASE_3_21
git_last_commit: 1e118c8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/STexampleData_1.16.0.tar.gz
vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html
vignetteTitles: STexampleData overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R
suggestsMe: BulkSignalR, escheR, ggsc, ggspavis, nnSVG, poem,
smoothclust, spatialSimGP, spoon, SpotSweeper, SVP, tpSVG
dependencyCount: 81
Package: SubcellularSpatialData
Version: 1.4.0
Depends: R (>= 4.4)
Imports: dplyr, hexbin, Matrix, SpatialExperiment, stats
Suggests: BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc,
rmarkdown, testthat (>= 3.0.0)
License: GPL (>= 3)
MD5sum: 5eed0418ba093f2d701c292db9f5e3f8
NeedsCompilation: no
Title: Annotated spatial transcriptomics datasets from 10x Xenium,
NanoString CosMx and BGI STOmics.
Description: This is a data package that hosts annotated sub-cellular
localised datasets from the STOmics, Xenium and CosMx
platforms. Specifically, it hosts datasets analysed in the
publication Bhuva et. al, 2024 titled "Library size confounds
biology in spatial transcriptomics data". Raw transcript
detections are hosted and functions to convert them to
SpatialExperiment objects have been implemented.
biocViews: ExperimentHub, SpatialData, Homo_sapiens_Data,
Mus_musculus_Data, LungCancerData
Author: Dharmesh D. Bhuva [aut, cre] (ORCID:
<https://orcid.org/0000-0002-6398-9157>)
Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva@adelaide.edu.au>
URL: https://davislaboratory.github.io/SubcellularSpatialData
VignetteBuilder: knitr
BugReports:
https://github.com/DavisLaboratory/SubcellularSpatialData/issues
git_url: https://git.bioconductor.org/packages/SubcellularSpatialData
git_branch: RELEASE_3_21
git_last_commit: a82e3d0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SubcellularSpatialData_1.4.0.tar.gz
vignettes:
vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.html
vignetteTitles: SubcellularSpatialData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.R
dependencyCount: 72
Package: SVM2CRMdata
Version: 1.40.0
Depends: R(>= 3.2.0)
License: LGPL (>= 2)
MD5sum: 2b65097e237228b521358ea985d06cd3
NeedsCompilation: no
Title: An example dataset for use with the SVM2CRM package
Description: An example dataset for use with the SVM2CRM package.
biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing,
DataImport
Author: Guidantonio Malagoli Tagliazucchi
Maintainer: Guidantonio Malagoli Tagliazucchi
<guidantonio.malagolitagliazucchi@unimore.it>
git_url: https://git.bioconductor.org/packages/SVM2CRMdata
git_branch: RELEASE_3_21
git_last_commit: 38a5ebd
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/SVM2CRMdata_1.40.0.tar.gz
vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf
vignetteTitles: The \Rpackage{SVM2CRMdata} Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R
dependencyCount: 0
Package: synapterdata
Version: 1.46.0
Depends: R (>= 2.10), synapter (>= 1.99.2)
Imports: utils
License: GPL-2
MD5sum: 99338464ce0e8dbfd596cffd647813ff
NeedsCompilation: no
Title: Data accompanying the synapter package
Description: Data independant acquisition of UPS1 protein mix in an E.
coli background obtained on a Waters Synapt G2 instrument.
biocViews: ExperimentData, MassSpectrometryData
Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/synapterdata
git_branch: RELEASE_3_21
git_last_commit: cff53db
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/synapterdata_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: synapter
dependencyCount: 150
Package: systemPipeRdata
Version: 2.12.2
Depends: R (>= 3.6.0)
Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes
Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools,
ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown,
systemPipeR, kableExtra, magrittr, dplyr
License: Artistic-2.0
MD5sum: 180fb83175214a32b0626bd8252ad988
NeedsCompilation: no
Title: systemPipeRdata: Workflow templates and sample data
Description: systemPipeRdata complements the systemPipeR workflow
management system (WMS) by offering a collection of
pre-designed data analysis workflow templates. These templates
are easily accessible and can be readily loaded onto a user's
system with a single command. Once loaded, the WMS can
immediately utilize these templates for efficient end-to-end
analysis, serving a wide range of data analysis needs.
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,
RiboSeq, WorkflowStep
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
URL: https://github.com/tgirke/systemPipeRdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/systemPipeRdata
git_branch: RELEASE_3_21
git_last_commit: 9ad596e
git_last_commit_date: 2025-05-26
Date/Publication: 2025-05-27
source.ver: src/contrib/systemPipeRdata_2.12.2.tar.gz
vignettes: vignettes/systemPipeRdata/inst/doc/new.html,
vignettes/systemPipeRdata/inst/doc/SPblast.html,
vignettes/systemPipeRdata/inst/doc/SPcheminfo.html,
vignettes/systemPipeRdata/inst/doc/SPscrna.html,
vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html
vignetteTitles: WF: Basic Generic Template, WF: BLAST Template, WF:
Cheminformatics Drug Similarity Template, WF: Basic Single Cell
Template, WF: ChIP-Seq Workflow Template, systemPipeRdata:
Workflow templates and sample data, WF: RIBO-Seq Workflow
Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/systemPipeRdata/inst/doc/new.R,
vignettes/systemPipeRdata/inst/doc/SPblast.R,
vignettes/systemPipeRdata/inst/doc/SPcheminfo.R,
vignettes/systemPipeRdata/inst/doc/SPscrna.R,
vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R
suggestsMe: systemPipeR, systemPipeShiny
dependencyCount: 26
Package: TabulaMurisData
Version: 1.26.0
Depends: R (>= 3.5)
Imports: ExperimentHub, utils
Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
License: MIT + file LICENSE
MD5sum: a93052397e1e39d5b7684f46c3feafd8
NeedsCompilation: no
Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium
Description: Access to processed 10x (droplet) and SmartSeq2 (on
FACS-sorted cells) single-cell RNA-seq data from the Tabula
Muris consortium (http://tabula-muris.ds.czbiohub.org/).
biocViews: SingleCellData, ExperimentData, RNASeqData
Author: Charlotte Soneson [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3833-2169>)
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TabulaMurisData
git_branch: RELEASE_3_21
git_last_commit: d4dcd5a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TabulaMurisData_1.26.0.tar.gz
vignettes: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.html
vignetteTitles: Tabula Muris data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.R
dependencyCount: 65
Package: TabulaMurisSenisData
Version: 1.14.0
Imports: ExperimentHub, SingleCellExperiment, HDF5Array,
SummarizedExperiment, gdata, AnnotationHub
Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle
License: MIT + file LICENSE
MD5sum: 25e608d975c2b9df8c4bdac0a193ce3f
NeedsCompilation: no
Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis
project
Description: This package provides access to RNA-seq data generated by
the Tabula Muris Senis project via the Bioconductor project.
The data is made available without restrictions by the Chan
Zuckerberg Biohub. It is provided here without further
processing, collected in the form of SingleCellExperiment
objects.
biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub
Author: Charlotte Soneson [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3833-2169>), Dania Machlab [aut]
(ORCID: <https://orcid.org/0000-0002-2578-6930>), Federico
Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>),
Stefania Astrologo [aut] (ORCID:
<https://orcid.org/0000-0002-4845-2802>)
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>
URL: https://github.com/fmicompbio/TabulaMurisSenisData
VignetteBuilder: knitr
BugReports: https://github.com/fmicompbio/TabulaMurisSenisData/issues
git_url: https://git.bioconductor.org/packages/TabulaMurisSenisData
git_branch: RELEASE_3_21
git_last_commit: 6383b22
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TabulaMurisSenisData_1.14.0.tar.gz
vignettes:
vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.html
vignetteTitles: TabulaMurisSenisData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.R
suggestsMe: SPOTlight
dependencyCount: 84
Package: TargetScoreData
Version: 1.44.0
Suggests: TargetScore, gplots
License: GPL-2
MD5sum: 40b2cd94dc15bcd37a0bb2e14283dd80
NeedsCompilation: no
Title: TargetScoreData
Description: Precompiled and processed miRNA-overexpression
fold-changes from 84 Gene Expression Omnibus (GEO) series
corresponding to 6 platforms, 77 human cells or tissues, and
113 distinct miRNAs. Accompanied with the data, we also
included in this package the sequence feature scores from
TargetScanHuman 6.1 including the context+ score and the
probabilities of conserved targeting for each miRNA-mRNA
interaction. Thus, the user can use these static sequence-based
scores together with user-supplied tissue/cell-specific
fold-change due to miRNA overexpression to predict miRNA
targets using the package TargetScore (download separately)
biocViews: ExperimentData, RNASeqData, miRNAData
Author: Yue Li
Maintainer: Yue Li <yueli@cs.toronto.edu>
git_url: https://git.bioconductor.org/packages/TargetScoreData
git_branch: RELEASE_3_21
git_last_commit: c2f138c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TargetScoreData_1.44.0.tar.gz
vignettes: vignettes/TargetScoreData/inst/doc/TargetScoreData.pdf
vignetteTitles: Processed human microRNA-overexpression data from GEO,,
and sequence information from TargetScan,, and targetScore from
TargetScore
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TargetScoreData/inst/doc/TargetScoreData.R
suggestsMe: TargetScore
dependencyCount: 0
Package: TargetSearchData
Version: 1.46.0
License: GPL (>= 2)
MD5sum: e654d6a0e4071a906103ebf41c0d7dcf
NeedsCompilation: no
Title: Example GC-MS data for TargetSearch Package
Description: Example files of GC-MS data for the TargetSearch Package.
The package contains raw NetCDF files from a E.coli salt stress
experiment, extracted peak lists, and sample metadata required
for a GC-MS analysis. The raw data has been restricted for
demonstration purposes.
biocViews: ExperimentData, Escherichia_coli_Data
Author: Alvaro Cuadros-Inostroza [aut, cre], Jan Lisec [aut], Henning
Redestig [aut], Matt Hannah [aut]
Maintainer: Alvaro Cuadros-Inostroza <acuadros+bioc@gmail.com>
URL: https://github.com/acinostroza/TargetSearchData
BugReports: https://github.com/acinostroza/TargetSearchData/issues
git_url: https://git.bioconductor.org/packages/TargetSearchData
git_branch: RELEASE_3_21
git_last_commit: 44972fe
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TargetSearchData_1.46.0.tar.gz
vignettes: vignettes/TargetSearchData/inst/doc/TargetSearchData.pdf
vignetteTitles: The TargetSearchData Package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TargetSearchData/inst/doc/TargetSearchData.R
suggestsMe: TargetSearch
dependencyCount: 0
Package: tartare
Version: 1.22.0
Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
Imports: utils
Suggests: BiocStyle, knitr, rmarkdown, testthat, tools
License: GPL-3
MD5sum: 772dcd008158d84ee926816d08d89ebc
NeedsCompilation: no
Title: Raw ground spectra recorded on Thermo Fisher Scientific mass
spectrometers
Description: Provides raw files recorded on different Liquid
Chromatography Mass Spectrometry (LC-MS) instruments. All
included MS instruments are manufactured by Thermo Fisher
Scientific and belong to the Orbitrap Tribrid or Q Exactive
Orbitrap family of instruments. Despite their common origin and
shared hardware components, e.g., Orbitrap mass analyser, the
above instruments tend to write data in different "dialects" in
a shared binary file format (.raw). The intention behind
tartare is to provide complex but slim real-world files that
can be used to make code robust with respect to this diversity.
In other words, it is intended for enhanced unit testing. The
package is considered to be used with the rawrr package and the
Spectra MsBackends.
biocViews: ExperimentData, MassSpectrometryData, ExperimentHub
Author: Christian Panse [aut, cre] (ORCID:
<https://orcid.org/0000-0003-1975-3064>), Tobias Kockmann [aut]
(ORCID: <https://orcid.org/0000-0002-1847-885X>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
URL: https://github.com/cpanse/tartare
VignetteBuilder: knitr
BugReports: https://github.com/cpanse/tartare/issues
git_url: https://git.bioconductor.org/packages/tartare
git_branch: RELEASE_3_21
git_last_commit: 73e34e7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tartare_1.22.0.tar.gz
vignettes: vignettes/tartare/inst/doc/tartare.html
vignetteTitles: make and use tartare data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tartare/inst/doc/tartare.R
suggestsMe: MsBackendRawFileReader, rawDiag, rawrr
dependencyCount: 65
Package: TBX20BamSubset
Version: 1.44.0
Depends: Rsamtools (>= 1.9.8)
Imports: xtable
License: LGPL
MD5sum: 81fae2376dc03d7becfc81eaab363896
NeedsCompilation: no
Title: Subset of BAM files from the "TBX20" experiment
Description: Dual transcriptional activator and repressor roles of
TBX20 regulate adult cardiac structure and function. A subset
of the RNA-Seq data.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: D. Bindreither
Maintainer: D. Bindreither <daniel.bindreither@gmail.com>
git_url: https://git.bioconductor.org/packages/TBX20BamSubset
git_branch: RELEASE_3_21
git_last_commit: fed74e5
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TBX20BamSubset_1.44.0.tar.gz
vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf
vignetteTitles: TBX20 RNA-Seq data subset
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R
importsMe: Rmmquant
suggestsMe: APAlyzer, magpie
dependencyCount: 40
Package: TCGAbiolinksGUI.data
Version: 1.28.0
Depends: R (>= 3.5.0)
Suggests: BiocStyle, knitr, rmarkdown, readr, DT
License: GPL-3
MD5sum: 083fa658bd03e5aa14b6446d3a8c7051
NeedsCompilation: no
Title: Data for the TCGAbiolinksGUI package
Description: Supporting data for the TCGAbiolinksGUI package.
biocViews: AssayDomainData, TechnologyData, OrganismData
Author: Tiago Chedraoui Silva
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>
URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data
VignetteBuilder: knitr
BugReports:
https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues
git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data
git_branch: RELEASE_3_21
git_last_commit: 487076b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TCGAbiolinksGUI.data_1.28.0.tar.gz
vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html
vignetteTitles: Supporting data for the TCGAbiolinksGUI package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R
importsMe: TCGAbiolinks
dependencyCount: 0
Package: TCGAcrcmiRNA
Version: 1.28.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: a48b5764a7bca20b4939c0cdecbb7f52
NeedsCompilation: no
Title: TCGA CRC 450 miRNA dataset
Description: colorectal cancer miRNA profile provided by TCGA
biocViews: ExperimentData, CancerData
Author: Claudio Isella
Maintainer: Claudio Isella <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA
git_branch: RELEASE_3_21
git_last_commit: 6b2fec9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TCGAcrcmiRNA_1.28.0.tar.gz
vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R
dependencyCount: 7
Package: TCGAcrcmRNA
Version: 1.28.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: 085553b8881bdddd90a2434b8b2badd2
NeedsCompilation: no
Title: TCGA CRC 450 mRNA dataset
Description: colorectal cancer mRNA profile provided by TCGA
biocViews: ExperimentData, CancerData
Author: Claudio Isella
Maintainer: Claudio Isella <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA
git_branch: RELEASE_3_21
git_last_commit: 32c742f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TCGAcrcmRNA_1.28.0.tar.gz
vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R
dependencyCount: 7
Package: TCGAMethylation450k
Version: 1.44.0
License: GPL-2
MD5sum: 7751dded01c83e3c2b4094b070a92663
NeedsCompilation: no
Title: The Cancer Genome Atlas Illumina 450k methylation example data
Description: The Cancer Genome Atlas (TCGA) is applying genomics
technologies to over 20 different types of cancer. This
package contains a small set of 450k array data in idat format.
biocViews: Genome, CancerData, MethylationArrayData
Author: Sean Davis
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
git_url: https://git.bioconductor.org/packages/TCGAMethylation450k
git_branch: RELEASE_3_21
git_last_commit: 3c04710
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TCGAMethylation450k_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: methylumi
dependencyCount: 0
Package: TCGAWorkflowData
Version: 1.32.0
Depends: R (>= 3.5.0)
Imports: SummarizedExperiment
Suggests: knitr, rmarkdown, pander, testthat, BiocStyle
License: GPL-3
MD5sum: 6afd7abf689232634081010b45213f83
NeedsCompilation: no
Title: Data for TCGA Workflow
Description: This experimental data package contains 11 data sets
necessary to follow the "TCGA Workflow: Analyze cancer genomics
and epigenomics data using Bioconductor packages".
biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData,
CancerData
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>
URL: https://f1000research.com/articles/5-1542/v2
VignetteBuilder: knitr
BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues
git_url: https://git.bioconductor.org/packages/TCGAWorkflowData
git_branch: RELEASE_3_21
git_last_commit: 9a3836c
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TCGAWorkflowData_1.32.0.tar.gz
vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html
vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer
genomics and epigenomics data using Bioconductor packages'
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R
dependencyCount: 36
Package: TENET.ExperimentHub
Version: 1.0.0
Depends: R (>= 4.5)
Imports: ExperimentHub, SummarizedExperiment, MultiAssayExperiment,
GenomicRanges, methods
Suggests: ExperimentHubData, testthat (>= 3.0.0), BiocManager, knitr,
rmarkdown, BiocStyle
License: GPL-2
MD5sum: 92f44611b47a1c1cf8f9338279844f7e
NeedsCompilation: no
Title: Experiment data for the TENET package
Description: ExperimentHub package containing datasets for use in the
TENET package's vignette and function examples. These include a
variety of different objects to illustrate different datasets
used in TENET functions. Where applicable, all datasets are
aligned to the hg38 human genome.
biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data,
CancerData, BreastCancerData, MicroarrayData, ExpressionData,
RNASeqData, MethylationArrayData, Genome, CellCulture, Tissue
Author: Rhie Lab at the University of Southern California [cre], Daniel
Mullen [aut] (ORCID: <https://orcid.org/0000-0002-7639-0549>),
Zexun Wu [aut] (ORCID:
<https://orcid.org/0000-0003-2566-1326>), Ethan Nelson-Moore
[aut] (ORCID: <https://orcid.org/0009-0001-6903-9232>), Suhn
Rhie [aut] (ORCID: <https://orcid.org/0000-0002-5522-5296>)
Maintainer: Rhie Lab at the University of Southern California
<rhielab@gmail.com>
URL: https://github.com/rhielab/TENET.ExperimentHub
VignetteBuilder: knitr
BugReports: https://github.com/rhielab/TENET.ExperimentHub/issues
git_url: https://git.bioconductor.org/packages/TENET.ExperimentHub
git_branch: RELEASE_3_21
git_last_commit: f3dd71d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENET.ExperimentHub_1.0.0.tar.gz
vignettes:
vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.html
vignetteTitles: Using the TENET.ExperimentHub datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.R
importsMe: TENET
dependencyCount: 78
Package: TENxBrainData
Version: 1.28.0
Depends: SingleCellExperiment, HDF5Array
Imports: AnnotationHub (>= 2.9.22), ExperimentHub
Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table, rmarkdown
License: CC BY 4.0
MD5sum: d50471aa78f1d02f4af292672373cf3e
NeedsCompilation: no
Title: Data from the 10X 1.3 Million Brain Cell Study
Description: Single-cell RNA-seq data for 1.3 million brain cells from
E18 mice, generated by 10X Genomics.
biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData
Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package
Maintainer [cre]
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TENxBrainData
git_branch: RELEASE_3_21
git_last_commit: 314de8a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENxBrainData_1.28.0.tar.gz
vignettes: vignettes/TENxBrainData/inst/doc/TENxBrainData.html
vignetteTitles: Exploring the 1.3 million brain cell scRNA-seq data
from 10X Genomics
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TENxBrainData/inst/doc/TENxBrainData.R
dependsOnMe: OSCA.advanced
suggestsMe: h5mread, HDF5Array
dependencyCount: 82
Package: TENxBUSData
Version: 1.22.0
Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics
Suggests: knitr, rmarkdown, BiocStyle
License: BSD_2_clause + file LICENSE
MD5sum: e2966fe503422cbb83c455144b7410ca
NeedsCompilation: no
Title: Single cell dataset from 10x in BUS format
Description: Download Barcode, UMI, and Set (BUS) format of 10x
datasets from within R. This package accompanies the package
BUSpaRse, which can load BUS format into R as a sparse matrix,
and which has utility functions related to using the C++
command line package bustools.
biocViews: SingleCellData, SequencingData, ExperimentHub,
ExperimentData, ExpressionData
Author: Lambda Moses [aut, cre] (ORCID:
<https://orcid.org/0000-0002-7092-9427>)
Maintainer: Lambda Moses <dlu2@caltech.edu>
URL: https://github.com/BUStools/TENxBUSData
VignetteBuilder: knitr
BugReports: https://github.com/BUStools/TENxBUSData/issues
git_url: https://git.bioconductor.org/packages/TENxBUSData
git_branch: RELEASE_3_21
git_last_commit: 285e716
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENxBUSData_1.22.0.tar.gz
vignettes:
vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.html
vignetteTitles: Downloading BUS data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.R
suggestsMe: BUSpaRse
dependencyCount: 65
Package: TENxPBMCData
Version: 1.26.0
Depends: SingleCellExperiment, HDF5Array
Imports: AnnotationHub, ExperimentHub
Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache,
BiocParallel
License: CC BY 4.0
MD5sum: 0877c5aa5d695d8b96373be5e5c16a53
NeedsCompilation: no
Title: PBMC data from 10X Genomics
Description: Single-cell RNA-seq data for on PBMC cells, generated by
10X Genomics.
biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentHub,
ExperimentData, SingleCellData
Author: Kasper D. Hansen [aut], Davide Risso [aut], Milan Malfait
[ctb], Jeroen Gilis [ctb], Theodore Killian [ctb], Murat Cem
Kose [ctb], Chong Tang [ctb], Teun van den Brand [ctb], Dania
Machlab [ctb], Stephanie Hicks [aut, cre]
Maintainer: Stephanie Hicks <shicks19@jhu.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TENxPBMCData
git_branch: RELEASE_3_21
git_last_commit: f213307
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENxPBMCData_1.26.0.tar.gz
vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html
vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R
dependsOnMe: OSCA.multisample, SingleRBook
importsMe: singleCellTK
suggestsMe: adverSCarial, ASURAT, celda, concordexR, decontX,
ExperimentSubset, glmGamPoi, iSEE, mbkmeans, schex, scone,
scry, sketchR, transformGamPoi
dependencyCount: 82
Package: TENxVisiumData
Version: 1.16.0
Depends: ExperimentHub, SpatialExperiment
Imports: utils
Suggests: BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: bff3737ceba780fd57a0c96d9a5dd1a7
NeedsCompilation: no
Title: Visium spatial gene expression data by 10X Genomics
Description: Collection of Visium spatial gene expression datasets by
10X Genomics, formatted into objects of class
SpatialExperiment. Data cover various organisms and tissues,
and include: single- and multi-section experiments, as well as
single sections subjected to both whole transcriptome and
targeted panel analysis. Datasets may be used for testing of
and as examples in packages, for tutorials and workflow
demonstrations, or similar purposes.
biocViews: ExperimentHub, ExpressionData, ExperimentData,
Homo_sapiens_Data, Mus_musculus_Data, ReproducibleResearch
Author: Helena L. Crowell [aut, cre] (ORCID:
<https://orcid.org/0000-0002-4801-1767>)
Maintainer: Helena L. Crowell <helena@crowell.eu>
URL: https://github.com/helenalc/TENxVisiumData
VignetteBuilder: knitr
BugReports: https://github.com/helenalc/TENxVisiumData/issues
git_url: https://git.bioconductor.org/packages/TENxVisiumData
git_branch: RELEASE_3_21
git_last_commit: e01f84e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENxVisiumData_1.16.0.tar.gz
vignettes: vignettes/TENxVisiumData/inst/doc/vignette.html
vignetteTitles: TENxVisiumData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TENxVisiumData/inst/doc/vignette.R
suggestsMe: SPOTlight
dependencyCount: 81
Package: TENxXeniumData
Version: 1.4.0
Depends: ExperimentHub
Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix,
SummarizedExperiment, utils
Suggests: BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 287cf7f916cb1277a05c99f457c9d3bb
NeedsCompilation: no
Title: Collection of Xenium spatial data by 10X genomics
Description: Collection of Xenium spatial transcriptomics datasets
provided by 10x Genomics, formatted into the Bioconductor
classes, the SpatialExperiment or SpatialFeatureExperiment
(SFE), to facilitate seamless integration into various
applications, including examples, demonstrations, and
tutorials. The constructed data objects include gene expression
profiles, per-transcript location data, centroid, segmentation
boundaries (e.g., cell or nucleus boundaries), and image.
biocViews: ExperimentData, ExperimentHub, SpatialData
Author: Matineh Rahmatbakhsh [aut, cre], Monica Ge [aut]
Maintainer: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
URL: https://github.com/mrbakhsh/TENxXeniumData
VignetteBuilder: knitr
BugReports: https://github.com/mrbakhsh/TENxXeniumData/issues
git_url: https://git.bioconductor.org/packages/TENxXeniumData
git_branch: RELEASE_3_21
git_last_commit: 3ac7b04
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TENxXeniumData_1.4.0.tar.gz
vignettes: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.html
vignetteTitles: TENxXeniumData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.R
suggestsMe: jazzPanda
dependencyCount: 165
Package: timecoursedata
Version: 1.18.0
Depends: R (>= 4.0), SummarizedExperiment
Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr,
BiocStyle
License: BSD 3-clause License + file LICENSE
MD5sum: 0394d29a45eb39571343da6d58d0f148
NeedsCompilation: no
Title: A data package for timecourse RNA-seq and microarray gene
expression data sets
Description: This data package contains timecourse gene expression data
sets. The first dataset, from Shoemaker et al, consists of
microarray samples from lung tissue of mice exposed to
different influenzy strains from 14 timepoints. The two other
datasets are leaf and root samples from sorghum crops exposed
to pre- and post-flowering drought stress and a control
condition, sampled across the plants lifetime.
biocViews: ExpressionData, MicroarrayData, RNASeqData
Author: Elizabeth Purdom [aut] (ORCID:
<https://orcid.org/0000-0001-9455-7990>), Nelle Varoquaux [aut,
cre] (ORCID: <https://orcid.org/0000-0002-8748-6546>)
Maintainer: Nelle Varoquaux <nelle.varoquaux@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/timecoursedata
git_branch: RELEASE_3_21
git_last_commit: 321d66e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/timecoursedata_1.18.0.tar.gz
vignettes: vignettes/timecoursedata/inst/doc/documentation.html
vignetteTitles: timecoursedata: Time course gene expression datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/timecoursedata/inst/doc/documentation.R
suggestsMe: moanin
dependencyCount: 36
Package: TimerQuant
Version: 1.38.0
Depends: shiny
Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit
Suggests: BiocStyle, reshape2, knitr, shinyBS
License: Artistic-2.0
MD5sum: 24836e9ad5bd569731f52570156da85f
NeedsCompilation: no
Title: Timer Quantification
Description: Supplementary Data package for tandem timer methods paper
by Barry et al. (2015) including TimerQuant shiny applications.
biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData,
Tissue
Author: Joseph Barry
Maintainer: Joseph Barry <joseph.barry@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TimerQuant
git_branch: RELEASE_3_21
git_last_commit: b916b21
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TimerQuant_1.38.0.tar.gz
vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf,
vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf
vignetteTitles: Supplementary Methods - automatic generation of paper
figures, Supplementary Methods - mathematical derivations
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R,
vignettes/TimerQuant/inst/doc/mathematicalDerivations.R
dependencyCount: 62
Package: tinesath1cdf
Version: 1.46.0
License: Artistic-2.0
MD5sum: 63fe4bef45f31110c6bffce81a5a7ed9
NeedsCompilation: no
Title: tinesath1cdf
Description: A package containing an environment represeting the
newcdf/tinesATH1.cdf.cdf file.
biocViews: Arabidopsis_thaliana_Data, ChipOnChipData
Author: Tine Casneuf
Maintainer: Tine Casneuf <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/tinesath1cdf
git_branch: RELEASE_3_21
git_last_commit: d78c7a8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tinesath1cdf_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: XhybCasneuf
dependencyCount: 0
Package: tinesath1probe
Version: 1.46.0
Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9)
License: LGPL
MD5sum: ee29a66ff4316134c290307b7b089372
NeedsCompilation: no
Title: Probe sequence data for microarrays of type tinesath1
Description: This package was automatically created by package
matchprobes version 1.4.0. The probe sequence data was obtained
from http://www.affymetrix.com.
biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData
Author: The Bioconductor Project www.bioconductor.org
Maintainer: Tine Casneuf <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/tinesath1probe
git_branch: RELEASE_3_21
git_last_commit: cac3c98
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tinesath1probe_1.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 45
Package: tissueTreg
Version: 1.28.0
Depends: R (>= 3.5)
Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment, ggplot2, reshape2
License: GPL (>= 2)
MD5sum: 31e370b510efc9051492708914be7063
NeedsCompilation: no
Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice
Description: The package provides ready to use epigenomes (obtained
from TWGBS) and transcriptomes (RNA-seq) from various tissues
as obtained in the study (Delacher and Imbusch 2017, PMID:
28783152). Regulatory T cells (Treg cells) perform two distinct
functions: they maintain self-tolerance, and they support organ
homeostasis by differentiating into specialized tissue Treg
cells. The underlying dataset characterises the epigenetic and
transcriptomic modifications for specialized tissue Treg cells.
biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData,
RNASeqData
Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus
Feuerer [aut], Benedikt Brors [aut]
Maintainer: Charles Imbusch <c.imbusch@dkfz.de>
URL: https://github.com/cimbusch/tissueTreg
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tissueTreg
git_branch: RELEASE_3_21
git_last_commit: 290bbb8
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tissueTreg_1.28.0.tar.gz
vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html
vignetteTitles: tissueTreg
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R
suggestsMe: DMRcate
dependencyCount: 0
Package: TMExplorer
Version: 1.18.0
Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache
Imports: methods, Matrix
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: 26f0268bc7c0a4577a5cb155f912815f
NeedsCompilation: no
Title: A Collection of Tumour Microenvironment Single-cell RNA
Sequencing Datasets and Corresponding Metadata
Description: This package provides a tool to search and download a
collection of tumour microenvironment single-cell RNA
sequencing datasets and their metadata. TMExplorer aims to act
as a single point of entry for users looking to study the
tumour microenvironment at the single cell level. Users can
quickly search available datasets using the metadata table and
then download the ones they are interested in for analysis.
biocViews: CancerData, SingleCellData, RNASeqData, SequencingData,
ExpressionData, GEO, PackageTypeData
Author: Erik Christensen [aut, cre], Alaine Naidas [aut], David Chen
[aut], Parisa Shooshtari [aut]
Maintainer: Erik Christensen <echris3@uwo.ca>
VignetteBuilder: knitr
BugReports: https://github.com/shooshtarilab/TMExplorer/issues
git_url: https://git.bioconductor.org/packages/TMExplorer
git_branch: RELEASE_3_21
git_last_commit: 143184d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TMExplorer_1.18.0.tar.gz
vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html
vignetteTitles: TMExplorer
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R
dependencyCount: 67
Package: tofsimsData
Version: 1.36.0
Depends: R (>= 3.2.0)
Suggests: knitr, rmarkdown, tools
License: GPL-3
MD5sum: 1648a2dccde3ede17035f5154354c678
NeedsCompilation: no
Title: Import, process and analysis of ToF-SIMS imaging data
Description: This packages contains data to be used with the 'tofsims'
package.
biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry,
DataImport
Author: Lorenz Gerber, Viet Mai Hoang
Maintainer: Lorenz Gerber <genfys@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tofsimsData
git_branch: RELEASE_3_21
git_last_commit: 6433bad
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tofsimsData_1.36.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: topdownrdata
Version: 1.30.0
Depends: topdownr
License: GPL (>= 3)
MD5sum: c552217514e9555806cb73057a515694
NeedsCompilation: no
Title: Example Files for the topdownr R Package
Description: Example data for the topdownr package generated on a
Thermo Orbitrap Fusion Lumos MS device.
biocViews: ExperimentData, MassSpectrometryData
Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard
Jensen [aut]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
URL: https://github.com/sgibb/topdownrdata/
BugReports: https://github.com/sgibb/topdownrdata/issues/
git_url: https://git.bioconductor.org/packages/topdownrdata
git_branch: RELEASE_3_21
git_last_commit: b78a03a
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/topdownrdata_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: topdownr
dependencyCount: 137
Package: TransOmicsData
Version: 1.4.0
Imports: S4Vectors, utils
Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo,
testthat, ExperimentHub
License: GPL-3 + file LICENSE
MD5sum: 4332b132e2875f485340db0a65b0dd41
NeedsCompilation: no
Title: A collection of trans-omics datasets across various biological
systems
Description: Contains a collection of trans-omics datasets generated
using various sequencing technologies such as RNA-seq, Mass
spectrometry and ChIP-seq. Modalities include the bulk
profiling of the phosphoproteome, proteome, transcriptome and
epigenome. Data reflects the timecourses of different
developmental systems from the mouse or human.
biocViews: ExperimentHub, MassSpectrometryData, RNASeqData,
ChIPSeqData, Tissue, SequencingData
Author: Carissa Chen [aut] (ORCID:
<https://orcid.org/0000-0003-2419-7840>), Di Xiao [aut, cre]
(ORCID: <https://orcid.org/0000-0002-9225-7086>), Pengyi Yang
[aut] (ORCID: <https://orcid.org/0000-0003-1098-3138>)
Maintainer: Di Xiao <d.xiao@sydney.edu.au>
URL: https://github.com/PYangLab/TransOmicsData
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/TransOmicsData
git_url: https://git.bioconductor.org/packages/TransOmicsData
git_branch: RELEASE_3_21
git_last_commit: 56bfd10
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TransOmicsData_1.4.0.tar.gz
vignettes:
vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.html
vignetteTitles: TransOmicsData: A collection of trans-omics datasets
across various biological systems
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.R
dependencyCount: 8
Package: tuberculosis
Version: 1.14.0
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr,
purrr, rlang, stringr, tibble, tidyr
Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown,
scater, usethis, utils
License: Artistic-2.0
MD5sum: 71c7f2d7372160e2307ba44ab43752f6
NeedsCompilation: no
Title: Tuberculosis Gene Expression Data for Machine Learning
Description: The tuberculosis R/Bioconductor package features
tuberculosis gene expression data for machine learning. All
human samples from GEO that did not come from cell lines, were
not taken postmortem, and did not feature recombination have
been included. The package has more than 10,000 samples from
both microarray and sequencing studies that have been processed
from raw data through a hyper-standardized, reproducible
pipeline.
biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data,
MicroarrayData, SequencingData, ReproducibleResearch
Author: Lucas Schiffer [aut, cre] (ORCID:
<https://orcid.org/0000-0003-3628-0326>)
Maintainer: Lucas Schiffer <schiffer.lucas@gmail.com>
URL: https://github.com/schifferl/tuberculosis
VignetteBuilder: knitr
BugReports: https://github.com/schifferl/tuberculosis/issues
git_url: https://git.bioconductor.org/packages/tuberculosis
git_branch: RELEASE_3_21
git_last_commit: 22d6906
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tuberculosis_1.14.0.tar.gz
vignettes: vignettes/tuberculosis/inst/doc/tuberculosis.html
vignetteTitles: tuberculosis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tuberculosis/inst/doc/tuberculosis.R
dependencyCount: 76
Package: TumourMethData
Version: 1.6.0
Depends: R (>= 4.2), SummarizedExperiment
Imports: ExperimentHub, GenomicRanges, HDF5Array, R.utils, rhdf5
Suggests: ggplot2, knitr, rmarkdown
License: Artistic-2.0
MD5sum: ae6e8a5d838ace8ba46a42aa0ec1cde9
NeedsCompilation: no
Title: A Collection of DNA Methylation Datasets for Human Tumour
Samples and Matching Normal Samples
Description: TumourMethData collects tumour methylation data from a
variety of different tumour types (and also matching normal
samples where available) and produced with different
technologies (e.g. WGBS, RRBS and methylation arrays) and
provides them as RangedSummarizedExperiments. This facilitates
easy extraction of methylation data for regions of interest
across different tumour types and studies.
biocViews: ExperimentData, ExperimentHub, MethylSeqData, CancerData,
Homo_sapiens_Data,
Author: Richard Heery [aut, cre] (ORCID:
<https://orcid.org/0000-0001-8067-3114>)
Maintainer: Richard Heery <richardheery@gmail.com>
URL: https://github.com/richardheery/TumourMethData
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/tag/TumourMethData
git_url: https://git.bioconductor.org/packages/TumourMethData
git_branch: RELEASE_3_21
git_last_commit: fe4e42d
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/TumourMethData_1.6.0.tar.gz
vignettes:
vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.html
vignetteTitles: getting_tumour_methylation_from_TumourMethData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.R
importsMe: methodical
dependencyCount: 84
Package: tweeDEseqCountData
Version: 1.46.0
Depends: Biobase, R (>= 4.3.0)
Suggests: knitr, BiocStyle, rmarkdown
License: MIT + file LICENSE
MD5sum: c12b5e537159f876c350e5aee000b24e
NeedsCompilation: no
Title: RNA-seq count data employed in the vignette of the tweeDEseq
package
Description: RNA-seq count data from Pickrell et al. (2010) employed to
illustrate the use of the Poisson-Tweedie family of
distributions with the tweeDEseq package.
biocViews: Genome, Homo_sapiens_Data, RNASeqData
Author: Dolors Pelegri-Siso [aut, cre] (ORCID:
<https://orcid.org/0000-0002-5993-3003>), Juan R. Gonzalez
[aut] (ORCID: <https://orcid.org/0000-0003-3267-2146>), Mikel
Esnaola [aut], Robert Castelo [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
URL: https://github.com/isglobal-brge/tweeDEseqCountData/
VignetteBuilder: knitr
BugReports: https://github.com/isglobal-brge/tweeDEseqCountData/issues
git_url: https://git.bioconductor.org/packages/tweeDEseqCountData
git_branch: RELEASE_3_21
git_last_commit: bf1977b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tweeDEseqCountData_1.46.0.tar.gz
vignettes:
vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.html
vignetteTitles: RNA-seq count data employed in the vignette of the
tweeDEseq package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.R
suggestsMe: GSAR, missMethyl, tweeDEseq, zenith
dependencyCount: 7
Package: tximportData
Version: 1.36.0
Suggests: knitr, markdown
License: GPL (>= 2)
MD5sum: 8043d6f2d8d6cf1777ddfee6ec3228ca
NeedsCompilation: no
Title: tximportData
Description: This package provides the output of running various
transcript abundance quantifiers on a set of 6 RNA-seq samples
from the GEUVADIS project. The quantifiers were Cufflinks,
RSEM, kallisto, Salmon and Sailfish. alevin example output is
also included. Forr details on version numbers, sample
information, and details on calls, see the package vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tximportData
git_branch: RELEASE_3_21
git_last_commit: 5545492
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/tximportData_1.36.0.tar.gz
vignettes: vignettes/tximportData/inst/doc/tximportData.html
vignetteTitles: Sample output files for tximport
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tximportData/inst/doc/tximportData.R
importsMe: TDbasedUFE
suggestsMe: DESeq2, eds, fishpond, tximeta, tximport, variancePartition
dependencyCount: 0
Package: VariantToolsData
Version: 1.32.0
Depends: R (>= 3.5.0), VariantAnnotation (>= 1.7.35)
Imports: BiocGenerics, GenomicRanges
Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle
License: Artistic-2.0
MD5sum: 3ec28a7c4500912080136d84ed9cc8ef
NeedsCompilation: no
Title: Data for the VariantTools tutorial
Description: Data from the sequencing of a 50/50 mixture of HapMap trio
samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53
region.
biocViews: ExperimentData, SequencingData, HapMap, SNPData
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
git_url: https://git.bioconductor.org/packages/VariantToolsData
git_branch: RELEASE_3_21
git_last_commit: a339056
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/VariantToolsData_1.32.0.tar.gz
vignettes: vignettes/VariantToolsData/inst/doc/intro.pdf
vignetteTitles: VariantTools Example Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VariantToolsData/inst/doc/intro.R
dependencyCount: 79
Package: VectraPolarisData
Version: 1.12.0
Depends: ExperimentHub, SpatialExperiment, utils
Suggests: BiocStyle, knitr, rmarkdown, dplyr
License: Artistic-2.0
MD5sum: c5b737c15dfebdcfa8b22f7f87e09985
NeedsCompilation: no
Title: Vectra Polaris and Vectra 3 multiplex single-cell imaging data
Description: Provides two multiplex imaging datasets collected on
Vectra instruments at the University of Colorado Anschutz
Medical Campus. Data are provided as a Spatial Experiment
objects. Data is provided in tabular form and has been
segmented and phenotyped using Inform software. Raw .tiff files
are not included.
biocViews: ExperimentHub, ExperimentData, SpatialData, SingleCellData,
Homo_sapiens_Data, ReproducibleResearch
Author: Wrobel Julia [aut, cre] (ORCID:
<https://orcid.org/0000-0001-6783-1421>), Tusharkanti Ghosh
[aut]
Maintainer: Wrobel Julia <julia.wrobel@cuanschutz.edu>
URL: https://github.com/julia-wrobel/VectraPolarisData
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/VectraPolarisData
git_url: https://git.bioconductor.org/packages/VectraPolarisData
git_branch: RELEASE_3_21
git_last_commit: a0fd37f
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/VectraPolarisData_1.12.0.tar.gz
vignettes: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.html
vignetteTitles: VectraPolarisData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.R
dependencyCount: 81
Package: vulcandata
Version: 1.30.0
Imports: utils
Suggests: viper
License: LGPL-3
MD5sum: 5641facedf7f52ee3267df11ae9c095d
NeedsCompilation: no
Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset
Description: This package provides a dummy regulatory network and
ChIP-Seq dataset for running examples in the vulcan package
biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData
Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
git_url: https://git.bioconductor.org/packages/vulcandata
git_branch: RELEASE_3_21
git_last_commit: be1b0ad
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/vulcandata_1.30.0.tar.gz
vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf
vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,,
dummy datasets
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R
suggestsMe: vulcan
dependencyCount: 1
Package: WeberDivechaLCdata
Version: 1.10.0
Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment
Imports: utils
Suggests: BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 00940f5ae5df35eb4f501de682f26b17
NeedsCompilation: no
Title: Spatially-resolved transcriptomics and single-nucleus
RNA-sequencing data from the locus coeruleus (LC) in postmortem
human brain samples
Description: Spatially-resolved transcriptomics (SRT) and
single-nucleus RNA-sequencing (snRNA-seq) data from the locus
coeruleus (LC) in postmortem human brain samples. Data were
generated with the 10x Genomics Visium SRT and 10x Genomics
Chromium snRNA-seq platforms. Datasets are stored in
SpatialExperiment and SingleCellExperiment formats.
biocViews: ExperimentData, ExperimentHub, ReproducibleResearch,
ExpressionData, SequencingData, RNASeqData, SingleCellData,
SpatialData, Homo_sapiens_Data
Author: Lukas M. Weber [aut, cre] (ORCID:
<https://orcid.org/0000-0002-3282-1730>), Heena R. Divecha
[aut] (ORCID: <https://orcid.org/0000-0002-1959-0675>)
Maintainer: Lukas M. Weber <lmweberedu@gmail.com>
URL: https://github.com/lmweber/WeberDivechaLCdata
VignetteBuilder: knitr
BugReports: https://github.com/lmweber/WeberDivechaLCdata/issues
git_url: https://git.bioconductor.org/packages/WeberDivechaLCdata
git_branch: RELEASE_3_21
git_last_commit: 8133353
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/WeberDivechaLCdata_1.10.0.tar.gz
vignettes:
vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.html
vignetteTitles: WeberDivechaLCdata package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.R
suggestsMe: nnSVG
dependencyCount: 81
Package: WES.1KG.WUGSC
Version: 1.40.0
License: GPL-2
MD5sum: adb0cee33d372eaccda927917eae1bff
NeedsCompilation: no
Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th
exon from the 1000 Genomes (1KG) Project by the Washington
University Genome Sequencing Center (WUGSC).
Description: The assembled .bam files of whole exome sequencing data
from the 1000 Genomes Project. 46 samples sequenced by the
Washington University Genome Sequencing Center are included.
biocViews: ExperimentData, Project1000genomes, SequencingData,
DNASeqData, Homo_sapiens_Data
Author: Yuchao Jiang, Nancy R. Zhang
Maintainer: Yuchao Jiang <yuchaoj@wharton.upenn.edu>
git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC
git_branch: RELEASE_3_21
git_last_commit: 2a03e4e
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/WES.1KG.WUGSC_1.40.0.tar.gz
vignettes: vignettes/WES.1KG.WUGSC/inst/doc/WES.1KG.WUGSC_vignettes.pdf
vignetteTitles: Using CODEX
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CODEX, iCNV
dependencyCount: 0
Package: WGSmapp
Version: 1.20.0
Depends: R (>= 3.6.0), GenomicRanges
License: GPL-2
MD5sum: d5f0393f0f2b71b770d52c33029bcd09
NeedsCompilation: no
Title: Mappability tracks of Whole-genome Sequencing from the ENCODE
Project
Description: This package provides whole-genome mappability tracks on
human hg19/hg38 assembly. We employed the 100-mers mappability
track from the ENCODE Project and computed weighted average of
the mappability scores if multiple ENCODE regions overlap with
the same bin. “Blacklist†bins, including segmental duplication
regions and gaps in reference assembly from telomere,
centromere, and/or heterochromatin regions are included. The
dataset consists of three assembled .bam files of single-cell
whole genome sequencing from 10X for illustration purposes.
biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData,
Homo_sapiens_Data, Genome, ENCODE
Author: Rujin Wang
Maintainer: Rujin Wang <rujin@email.unc.edu>
git_url: https://git.bioconductor.org/packages/WGSmapp
git_branch: RELEASE_3_21
git_last_commit: 562f0a1
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/WGSmapp_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: SCOPE
dependencyCount: 23
Package: xcoredata
Version: 1.12.0
Depends: R (>= 4.2)
Imports: ExperimentHub (>= 2.2.0), utils (>= 4.2.0)
Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2),
GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges
(>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>=
1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3),
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore
License: GPL-2
MD5sum: 4857b08056b023e6a4c4f64618bc1e1c
NeedsCompilation: no
Title: data package for xcore
Description: Provides data to use with xcore package.
biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data
Author: Maciej Migdał [aut, cre] (ORCID:
<https://orcid.org/0000-0002-8021-7263>), Bogumił Kaczkowski
[aut] (ORCID: <https://orcid.org/0000-0001-6554-5608>)
Maintainer: Maciej Migdał <mcjmigdal@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/xcoredata
git_branch: RELEASE_3_21
git_last_commit: 6e7544b
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/xcoredata_1.12.0.tar.gz
vignettes: vignettes/xcoredata/inst/doc/xcoredata.html
vignetteTitles: xcoredata
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/xcoredata/inst/doc/xcoredata.R
suggestsMe: xcore
dependencyCount: 65
Package: XhybCasneuf
Version: 1.46.0
Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
License: Artistic-2.0
MD5sum: 2a1cd9a3a2a649c095b3cfcacd3bf3e4
NeedsCompilation: no
Title: EBI/PSB cross-hybridisation study package
Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip
biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData
Author: Tineke Casneuf <tine@ebi.ac.uk>
Maintainer: Tineke Casneuf <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/XhybCasneuf
git_branch: RELEASE_3_21
git_last_commit: abef7e0
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/XhybCasneuf_1.46.0.tar.gz
vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf
vignetteTitles: Xhyb
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R
dependencyCount: 53
Package: yeastCC
Version: 1.48.0
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: fb9396dbcff7442cb6fc4b047b57ccc8
NeedsCompilation: no
Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell
cycle microarray data
Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle
microarray experiment
biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data,
CancerData, MicroarrayData, OneChannelData, GEO
Author: Sandrine Dudoit <sandrine@stat.berkeley.edu>
Maintainer: Sandrine Dudoit <sandrine@stat.berkeley.edu>
git_url: https://git.bioconductor.org/packages/yeastCC
git_branch: RELEASE_3_21
git_last_commit: 8708bd9
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/yeastCC_1.48.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: LiquidAssociation
suggestsMe: fastLiquidAssociation, ibh
dependencyCount: 7
Package: yeastExpData
Version: 0.54.0
Depends: R (>= 2.4), graph (>= 1.9.26)
Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db
License: GPL
MD5sum: 2c4ec07b7b9109c7107cc68a0f31a478
NeedsCompilation: no
Title: Yeast Experimental Data
Description: A collection of different sets of experimental data from
yeast.
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data
Author: R. Gentleman
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/yeastExpData
git_branch: RELEASE_3_21
git_last_commit: b7cdb14
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/yeastExpData_0.54.0.tar.gz
vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf
vignetteTitles: Yeast PPI Example
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R
dependsOnMe: PPInfer
suggestsMe: ClusterJudge
dependencyCount: 8
Package: yeastGSData
Version: 0.46.0
License: Artistic-2.0
MD5sum: 5b1c31d508932827393ff0978171504a
NeedsCompilation: no
Title: Yeast Gold Standard Data
Description: A collection of so-called gold (and other) standard data
sets
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data
Author: R. Gentleman
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/yeastGSData
git_branch: RELEASE_3_21
git_last_commit: 10ec2b7
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/yeastGSData_0.46.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: yeastNagalakshmi
Version: 1.44.0
License: Artistic-2.0
MD5sum: a2c47b7dbd6cca227e698d146d3c0af4
NeedsCompilation: no
Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al.
Description: The yeast genome data was retrieved from the sequence read
archive, aligned with bwa, and converted to BAM format with
samtools.
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data,
SequencingData, BiocViews, ChIPSeqData
Author: Martin Morgan <mtmorgan@fhcrc.org>
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
git_url: https://git.bioconductor.org/packages/yeastNagalakshmi
git_branch: RELEASE_3_21
git_last_commit: 9f9f354
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/yeastNagalakshmi_1.44.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ShortRead
dependencyCount: 0
Package: yeastRNASeq
Version: 0.46.0
Depends: R (>= 2.4)
Suggests: Biobase, ShortRead, IRanges
License: GPL
MD5sum: 068cb630330c43f4df6e3ec36b889a89
NeedsCompilation: no
Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008
Description: A selection of RNA-Seq data from a yeast transcriptome
experiment.
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data,
SequencingData, RNASeqData
Author: James H. Bullard and Kasper D. Hansen
Maintainer: J. Bullard <bullard@stat.berkeley.edu>
git_url: https://git.bioconductor.org/packages/yeastRNASeq
git_branch: RELEASE_3_21
git_last_commit: e03e849
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/yeastRNASeq_0.46.0.tar.gz
vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf
vignetteTitles: An overview of yeastRNASeq
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R
suggestsMe: EDASeq
dependencyCount: 0
Package: zebrafishRNASeq
Version: 1.28.0
Depends: R (>= 2.10)
Suggests: BiocStyle, knitr
License: GPL
MD5sum: 746cf6653e5c0af5e58628d083281e79
NeedsCompilation: no
Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014)
Description: Gene-level read counts from RNA-Seq for gallein-treated
and control zebrafish.
biocViews: ExperimentData, Danio_rerio_Data, RNASeqData
Author: Davide Risso
Maintainer: Davide Risso <risso.davide@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/zebrafishRNASeq
git_branch: RELEASE_3_21
git_last_commit: 5724332
git_last_commit_date: 2025-04-15
Date/Publication: 2025-04-17
source.ver: src/contrib/zebrafishRNASeq_1.28.0.tar.gz
vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.html
vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level
Counts
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R
suggestsMe: RUVSeq, sva
dependencyCount: 0
Package: curatedCRCData
Version: 2.40.0
Depends: R (>= 2.10.0), nlme
Imports: BiocGenerics
Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
License: Artistic-2.0
Title: Colorectal Cancer Gene Expression Analysis
Description: The curatedCRC package provides relevant functions and
data for gene expression analysis in patients with colorectal
cancer.
biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData
Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi
Waldron
Maintainer: Princy Parsana <princyparsana@jhu.edu>
URL: https://bitbucket.org/biobakery/curatedcrcdata