GenomeInfoDb
This is the released version of GenomeInfoDb; for the devel version, see GenomeInfoDb.
All Bioconductor versions of GenomeInfoDb
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Bioconductor version: 3.23 · Package version: 1.48.0
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
From within R, enter citation("GenomeInfoDb"):
Sonali Arora, Martin Morgan, Marc Carlson, Hervé Pagès. GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style. doi:10.18129/B9.bioc.GenomeInfoDb, R package version 1.48.0, https://bioconductor.org/packages/GenomeInfoDb.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomeInfoDb")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.48.0 |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/GenomeInfoDb |
| Bug Reports | https://github.com/Bioconductor/GenomeInfoDb/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12 years) |
| Downloads rank | 19 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software |
| Package Short Url | https://bioconductor.org/packages/GenomeInfoDb/ |
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 |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GenomeInfoDb_1.48.0.tar.gz |
| Windows binary (x86_64) | GenomeInfoDb_1.48.0.zip |
| macOS binary (arm64) | GenomeInfoDb_1.48.0.tgz |
| macOS binary (x86_64) | GenomeInfoDb_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomeInfoDb |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomeInfoDb |
| Package Downloads Report | Download Stats |
Dependencies
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
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
Reverse dependencies
Depends On Me (10): annotation, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenomeForge, CODEX, IdeoViz, liftOver, SCOPE, UCSCRepeatMasker, variants
Imports Me (201): ActiveDriverWGS, AllelicImbalance, annoLinker, AnnotationHubData, atacInferCnv, ATACseqQC, atena, BaalChIP, bambu, Banksy, bedbaser, BindingSiteFinder, biovizBase, biscuiteer, breakpointR, BUSpaRse, cageminer, cardelino, cfdnakit, cfDNAPro, chimeraviz, ChIPanalyser, chipenrich.data, ChIPpeakAnno, ChIPseeker, circRNAprofiler, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, comapr, CopyNumberPlots, crisprDesign, crispRdesignR, CrispRVariants, customProDB, damidBind, Damsel, derfinder, derfinderPlot, DEScan2, DESNP, diffHic, diffUTR, DMRcaller, DOTSeq, driveR, DuplexDiscovereR, easylift, ensembldb, EpiCompare, epigenomix, epimutacions, epiregulon, epiRomics, epiSeeker, epivizr, EventPointer, extraChIPs, factR, fastRanges, fitCons.UCSC.hg19, fourSynergy, fRagmentomics, FRASER, funtooNorm, GA4GHshiny, gDNAx, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicPlot, GenomicScores, ggbio, GOaGO, GRaNIE, grasp2db, GUIDEseq, Gviz, gwascat, h5vc, HiCaptuRe, HiCDCPlus, HiContacts, hicream, idr2d, igblastr, InPAS, karyoploteR, karyotapR, katdetectr, linkSet, locuszoomr, 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, mariner, metagene2, metaseqR2, methimpute, methodical, MethylSeekR, MethylSeqData, methylumi, missMethyl, mobileRNA, Motif2Site, motifbreakR, mSigSpectra, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, normr, ocrRBBR, OGRE, ORFik, parati, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, plotgardener, proActiv, profileplyr, ProteoDisco, PureCN, R3CPET, raer, RareVariantVis, RCAS, RcisTarget, recount, regioneR, regionReport, RESOLVE, revert, rGREAT, ribosomeProfilingQC, roar, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, SEMPLR, seqCAT, SGSeq, Signac, signeR, SigsPack, Site2Target, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, SOMNiBUS, SparseSignatures, SPICEY, spiky, SpliceWiz, STADyUM, StructuralVariantAnnotation, svaNUMT, svaRetro, TAPseq, TCGAutils, tepr, tidyCoverage, TmCalculator, TnT, trackViewer, transcriptR, txdbmaker, Ularcirc, UMI4Cats, UPDhmm, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me (76): AlphaMissenseR, AnnotationForge, AnnotationHub, annotatr, BgeeCall, BioMartGOGeneSets, BSgenome, bumphunter, Chicago, CNVScope, crupR, CTCF, dar, DEXSeq, DFplyr, DiffBind, DMRcate, enhancerHomologSearch, epialleleR, epigraHMM, excluderanges, ExperimentHubData, fishpond, GA4GHclient, GENESIS, GenomicFeatures, GenomicRanges, GenomicTuples, gkmSVM, gmapR, gmoviz, GRIN2, gwas2crispr, HelloRanges, HicAggR, icetea, jazzPanda, LACHESIS, ldblock, megadepth, methrix, multicrispr, nullranges, Organism.dplyr, OUTRIDER, parglms, peakCombiner, PICB, PlinkMatrix, plyinteractions, polyRAD, QDNAseq, RaggedExperiment, RapidoPGS, recoup, regioneReloaded, rtracklayer, scGraphVerse, scLANE, scTreeViz, Seqinfo, seqpac, seqsetvis, sesame, sesameData, Seurat, sitadela, SomaticSignatures, splatter, SummarizedExperiment, systemPipeR, TEKRABber, treeclimbR, UCSC.utils, VariantAnnotation, xcoredata