DOI: 10.18129/B9.bioc.GenomeInfoDb    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb.

Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: 3.7

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, Martin Morgan, Marc Carlson, H. Pagès

Maintainer: Bioconductor Package Maintainer <maintainer at>

Citation (from within R, enter citation("GenomeInfoDb")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script GenomeInfoDb: Introduction to GenomeInfoDb
PDF R Script GenomeInfoDb: Submitting your organism to GenomeInfoDb
PDF   Reference Manual
Text   NEWS
Video   Simple tasks genomeInfoDb


biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.16.0
In Bioconductor since BioC 2.14 (R-3.1) (4.5 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12)
Imports stats, stats4, utils, RCurl, GenomeInfoDbData
Suggests GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
Depends On Me BSgenome, bumphunter, ChIPComp, CODEX, CSAR, eQTL, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, htSeqTools, IdeoViz, methyAnalysis, Rsamtools, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ATACseqQC, BaalChIP, ballgown, BasicSTARRseq, biovizBase, BiSeq, bnbc, branchpointer, BSgenome, bsseq, CAGEfightR, CAGEr, casper, CexoR, chimeraviz, chipenrich,, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, cn.mops, CNEr, CNPBayes, CNVPanelizer, compEpiTools, consensusSeekeR, conumee, CopywriteR, CrispRVariants, csaw, customProDB, DeepBlueR, derfinder, derfinderPlot, DEScan2, diffHic, diffloop, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, ensembldb, ensemblVEP, epigenomix, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, fitCons.UCSC.hg19, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicFiles, GenomicInteractions, GenomicScores, genoset, genotypeeval, GenVisR, ggbio, GGtools, GoogleGenomics, gQTLstats, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiTC, HTSeqGenie, IMAS, InPAS, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.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.r2.0.1.GRCh38, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, metagene, metavizr, methimpute, methInheritSim, methylKit, methylPipe, methylumi, methyvim, minfi, MinimumDistance, mosaics, motifbreakR, motifmatchr, msgbsR, MutationalPatterns, myvariant, NADfinder, NarrowPeaks, normr, nucleR, ORFik, Organism.dplyr, panelcn.mops, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, plyranges, podkat, prebs, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RareVariantVis, Rariant, Rcade, RCAS, rCGH, recount, regioneR, regionReport, Repitools, RiboProfiling, riboSeqR, RJMCMCNucleosomes, roar, RTCGAToolbox, rtracklayer, scmeth, segmentSeq, SeqArray, seqCAT, seqplots, sevenC, SGSeq, ShortRead, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticSignatures, SparseSignatures, SplicingGraphs, SPLINTER, srnadiff, STAN, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TCGAutils, TCGAWorkflow, TFBSTools, TFutils, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, TxRegInfra, VanillaICE, VariantFiltering, VariantTools, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA, yriMulti
Suggests Me AnnotationForge, AnnotationHub, BiocOncoTK, chromswitch, ExperimentHubData, gQTLBase, QDNAseq, recoup
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GenomeInfoDb_1.16.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) GenomeInfoDb_1.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: