GenomeInfoDb
This is the development version of GenomeInfoDb; for the stable release version, see GenomeInfoDb.
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Bioconductor version: Development (3.23)
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Author: Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Hervé Pagès [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb] (vignette translation from Sweave to Rmarkdown / HTML), Emmanuel Chigozie Elendu [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("GenomeInfoDb")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GenomeInfoDb")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomeInfoDb")| GenomeInfoDb: Introduction to GenomeInfoDb | R Script | |
| Submitting your organism to GenomeInfoDb | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| Video |
Details
| biocViews | Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, BiocGenerics(>= 0.53.2), S4Vectors(>= 0.47.6), IRanges(>= 2.41.1), Seqinfo(>= 0.99.2) |
| Imports | stats, utils, UCSC.utils |
| System Requirements | |
| URL | https://bioconductor.org/packages/GenomeInfoDb |
| Bug Reports | https://github.com/Bioconductor/GenomeInfoDb/issues |
See More
| Suggests | GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | CODEX, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, UCSCRepeatMasker |
| Imports Me | BaalChIP, Banksy, breakpointR, cfdnakit, CNVPanelizer, CrispRVariants, GenomicDistributions, GenomicScores, h5vc, HiContacts, idr2d, igblastr, methimpute, multiHiCcompare, Site2Target, TnT, VanillaICE, VplotR, fitCons.UCSC.hg19, grasp2db, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v4.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, BioPlex, GenomicDistributionsData, MethylSeqData, crispRdesignR, driveR, hicream, ICAMS, karyotapR, locuszoomr, MAAPER, Signac, tepr |
| Suggests Me | AlphaMissenseR, AnnotationForge, AnnotationHub, Chicago, dar, DEXSeq, DFplyr, epialleleR, fishpond, GenomicRanges, GenomicTuples, jazzPanda, ldblock, megadepth, parglms, peakCombiner, PICB, QDNAseq, RaggedExperiment, scGraphVerse, scLANE, Seqinfo, sesame, splatter, SummarizedExperiment, systemPipeR, treeclimbR, UCSC.utils, BioMartGOGeneSets, CTCF, excluderanges, sesameData, xcoredata, gkmSVM, GRIN2, polyRAD, Seurat |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomeInfoDb_1.47.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomeInfoDb |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomeInfoDb |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomeInfoDb/ |
| Package Short Url | https://bioconductor.org/packages/GenomeInfoDb/ |
| Package Downloads Report | Download Stats |