R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 4.1), minfi(>= 1.36.0), ExperimentHub
R (>= 3.6.0), SummarizedExperiment, ExperimentHub
R (>= 3.6), SummarizedExperiment, ExperimentHub
R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment,
RaggedExperiment
R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0)
R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
R (>= 4.0), Biobase, GSEABase, SummarizedExperiment
R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots,
limma, vcd, LSD,EBImage
R (>= 4.4.0), SingleCellExperiment, SpatialExperiment,
cytomapper,
R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
R (>= 4.2.0), EBImage, SpatialExperiment
R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R
(>= 3.6.0)
SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment,
MultiAssayExperiment
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 4.1), SingleCellExperiment, SummarizedExperiment,
SpatialExperiment
R (>= 3.6), ExperimentHub, SingleCellExperiment
R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0),
Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4),
ShortRead (>= 1.41)
R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet
R (>= 4.1), SummarizedExperiment, ExperimentHub
R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors, zellkonverter
AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment,
SingleCellExperiment, SummarizedExperiment
R (>= 4.3.0), ExperimentHub, AnnotationHub
R (>= 4.1), ExperimentHub, SummarizedExperiment
SpatialExperiment (>= 1.3.3), R (>= 4.1)
R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
R (>= 4.1), SingleCellExperiment, BiocFileCache
R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage,
magick, magrittr, filesstrings, animation, einsum
BiocFileCache, GEOquery, graph, methods, utils
beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
dplyr, utils, purrr, stringr, tidyr, tidyselect,
BiocFileCache, httr2, tools, S4Vectors
utils, methods, Matrix, ExperimentHub, AnnotationHub,
AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats,
gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI,
RSQLite, jsonlite
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia,
purrr, rlang, stringr, tibble, tidyr, tidyselect
ExperimentHub, AnnotationHub, utils, methods, rlang, stats,
reshape2
AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang,
stats
AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors,
stats, SummarizedExperiment, utils
utils, stats, tools, sesame, methods, sesameData,
BiocParallel, BiocManager
utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2,
curl, tibble
affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs,
sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr,
survival, gplots, AnnotationDbi, Biobase
GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
BiocFileCache, S4Vectors, rjson, utils, tools
ExperimentHub, SummarizedExperiment, AnnotationHub, utils,
glue, S4Vectors, scater
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
SummarizedExperiment, Seurat, SingleCellExperiment,
AnnotationHub, ExperimentHub, ggplot2
BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
genefilter, nlme, quadprog, graphics, stats, utils,
AnnotationHub, SummarizedExperiment, S4Vectors
SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils,
AnnotationHub
BiocFileCache, HiCExperiment, GenomicRanges, IRanges,
S4Vectors, utils, tools
RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools
ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter,
data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ensembldb
ExperimentHub, SingleCellExperiment, SpatialExperiment,
HDF5Array, SummarizedExperiment, S4Vectors, htmltools,
rmarkdown, base64enc, utils
dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k,
minfi, utils, AnnotationHub, SummarizedExperiment
AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr,
kableExtra, knitr, magrittr, methods, readr, stringr, tibble,
utils
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
methods, utils, ExperimentHub, S4Vectors, DelayedArray,
HDF5Array
ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr,
tidyr, purrr, utils
GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
animalcules, data.table, dplyr, ggplot2, magrittr,
MultiAssayExperiment, plyr, rlang, S4Vectors, stringr,
SummarizedExperiment, tibble, tidyr, tidyselect
grDevices, AnnotationHub, BumpyMatrix, ExperimentHub,
S4Vectors, SingleCellExperiment, SummarizedExperiment,
HDF5Array
BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr,
ggplot2, magrittr, Matrix, MultiAssayExperiment, purrr,
Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr,
SummarizedExperiment, taxonomizr, tibble, tidyr, tools
ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
BiocFileCache, tools, S4Vectors, ape, utils
methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix
ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db,
AnnotationDbi, methods, stats, AnnotationHub
AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array,
stringr, SummarizedExperiment
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
ExperimentHub, AnnotationHub, dplyr, purrr, queryup, spdl,
tidyr, tidyselect, stringr, lifecycle, rlang, htmltools
ExperimentHub, Rsamtools, BiocGenerics, rtracklayer,
SingleCellExperiment
AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate,
methods, rhdf5, alabaster.matrix
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
utils, readr, stringr, GenomicRanges (>= 1.61.1), S4Vectors,
IRanges, Seqinfo
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, rhdf5
AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub,
graphics, HDF5Array, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
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
dplyr, hexbin, Matrix, SpatialExperiment, stats
methods, Biostrings, BiocGenerics, jsonlite, remotes
ExperimentHub, SingleCellExperiment, HDF5Array,
SummarizedExperiment, gdata, AnnotationHub
ExperimentHub, SummarizedExperiment, MultiAssayExperiment,
GenomicRanges, methods
SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix,
SummarizedExperiment, utils
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr,
purrr, rlang, stringr, tibble, tidyr
Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq,
ExperimentHub, depmap, knitr, rmarkdown
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
DT, forcats, ggplot2, htmltools, knitr, rmarkdown,
sessioninfo, testthat, EnrichmentBrowser,
MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub,
methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate,
BiocManager, ensembldb
BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>=
3.0.0)
knitr, rmarkdown, BiocStyle, AnnotationHub, TFEA.ChIP,
DESeq2, testthat (>= 3.0.0)
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
clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr,
BiocStyle
knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi,
S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr,
tidyr, ggplot2
knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr,
dplyr, tidyr, ggplot2, S4Vectors
BiocStyle, survival, xtable, sva, genefilter, logging
survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle, knitr, rmarkdown
BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat,
utils, uwot, vegan, OmicsMLRepoR, lefser
BiocStyle, futile.logger, genefilter, knitr, logging,
metafor, rmarkdown, RUnit, survival, sva, xtable
BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer,
ComplexHeatmap, corrplot, formatR
BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown,
SummarizedExperiment, sva, testthat
BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
tibble, BiocStyle, randomForest, testthat, knitr, rmarkdown,
e1071, xgboost, keras, tensorflow
knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, stringr, tidyverse, magick
sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
dplyr, testthat, methods, BiocStyle, knitr, rmarkdown
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
BiocStyle, knitr, rmarkdown, testthat, DropletUtils
knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
BiocStyle, knitr, dplyr, devtools, DT, rmarkdown
testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle,
Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
BiocFileCache, SeuratObject, knitr, rmarkdown, googledrive,
BiocStyle, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics
rmarkdown, BiocStyle, knitr, ExperimentHub, minfi
affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter
knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown,
rbibutils, testthat (>= 3.0.0)
knitr, rmarkdown, BiocGenerics, sva, BiocManager
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
FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
rtracklayer, dplyr, testthat, methods, BiocStyle, knitr,
rmarkdown
BiocStyle, gDRstyle (>= 1.7.1), knitr, qs2, reshape2,
rmarkdown, SummarizedExperiment, testthat, yaml
limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
SummarizedExperiment, SingleCellExperiment
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown
ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown,
testthat, minfi, tibble, sessioninfo
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
DESeq2
BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3)
AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, scuttle, Rtsne, igraph, iSEE, testthat
knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac,
zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust
RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown
testthat, methods, BiocStyle, knitr, rmarkdown
Biobase, BiocCheck, BiocManager, BiocStyle, circlize,
cowplot, dendextend, devtools, ggplot2, gridExtra, haven,
phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
testthat (>= 3.0.0), sessioninfo, rmarkdown, knitr,
BiocStyle, ExperimentHubData, AnnotationHubData, RefManageR
testthat, knitr, rmarkdown, ggplot2, ggrepel
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
BiocStyle, knitr, rmarkdown, markdown, testthat
knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0),
rmarkdown
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
LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat
knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0)
grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore,
terra, testthat, BiocStyle, DropletUtils
testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
testthat, knitr, BiocStyle, rmarkdown, markdown
animalcules, BiocStyle, biomformat, GenomicRanges, IRanges,
knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread,
spelling, sys, testthat, usethis
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia,
ggplot2, tidyr, dplyr, magrittr, tibble, purrr
knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown,
testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2)
MSnbase, xcms (>= 3.13.8), CAMERA, knitr, Heatplus,
pcaMethods, sp, rmarkdown, Biobase
BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment
BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
SpatialExperiment, ggplot2, BiocStyle, knitr, rmarkdown,
R.utils
knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments,
Rsamtools
knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors,
devtools, testthat
BiocStyle, ggplot2, knitr, rmarkdown, testthat
knitr, rmarkdown, markdown, BiocStyle, preciseTAD
pRoloc (>= 1.13.8), testthat, SummarizedExperiment
tibble, BiocStyle, knitr, testthat (>= 3.0.0),
ComplexHeatmap, circlize, pals, ggplot2 (>= 3.5.0), grDevices,
ggExtra, bio3d, r3dmol, forcats, ggdist (>= 3.3.0)
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
knitr, testthat, BiocStyle, rcellminer, rmarkdown
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
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,
corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz,
genefilter, plotly, gridExtra, dplyr, lubridate, magick,
cleaver
knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
knitr, rmarkdown, markdown, SingleCellAlleleExperiment,
Matrix, BiocStyle
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi,
testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, jsonvalidate,
BiocManager
BiocGenerics, GenomeInfoDb, sesame, testthat, knitr,
rmarkdown
Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl,
BiocStyle
BiocStyle, knitr, rmarkdown, SeuratObject,
SpatialFeatureExperiment, testthat (>= 3.0.0)
DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr, BiocParallel
BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown,
scater, scran, UpSetR, uwot
AnnotationHubData, BiocStyle, ExperimentHub,
ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0)
knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer
BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array
BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc,
rmarkdown, testthat (>= 3.0.0)
GenomicFeatures, DT, txdbmaker, GenomicRanges, IRanges,
Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr,
rmarkdown, systemPipeR, kableExtra, magrittr, dplyr, gert
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, tools
knitr, rmarkdown, pander, testthat, BiocStyle
TENET, ExperimentHubData, testthat (>= 3.0.0), BiocManager,
knitr, rmarkdown, BiocStyle
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table, rmarkdown
rmarkdown, knitr, BiocStyle, snow, BiocFileCache,
BiocParallel
testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment, ggplot2, reshape2
BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo,
testthat, ExperimentHub
BiocStyle, ggplot2, knitr, readr, rmarkdown, scater, usethis,
utils
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle