Representation and manipulation of genomic intervals

Bioconductor version: Development (3.0)

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals. Specialized containers for representing and manipulating short alignments against a reference genome are defined in the GenomicAlignments package.

Author: P. Aboyoun, H. Pages and M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at>

To install this package, start R and enter:


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


PDF R Script An Introduction to GenomicRanges
PDF R Script GenomicRanges HOWTOs
PDF   Reference Manual
Text   NEWS


biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.17.26
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.1.0), IRanges(>= 1.99.21), GenomeInfoDb(>= 1.1.3)
Imports methods, utils, stats, BiocGenerics, IRanges, XVector
Suggests AnnotationDbi(>= 1.21.1), AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, Biostrings(>= 2.25.3), Rsamtools(>= 1.13.53), GenomicAlignments, rtracklayer, KEGG.db, KEGGgraph, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, seqnames.db, org.Sc.sgd.db, VariantAnnotation, edgeR, DESeq, DEXSeq, pasilla, pasillaBamSubset, RUnit, digest, BiocStyle
System Requirements
Depends On Me AllelicImbalance, annmap, Basic4Cseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, bumphunter, CAFE, casper, cheung2010, chimera, ChIPQC, chipseq, cleanUpdTSeq, cn.mops, COPDSexualDimorphism, CSAR, DASiR, deepSNV, DESeq2, DEXSeq, DiffBind, DMRforPairs, DREAM4, dsQTL, EatonEtAlChIPseq, ensemblVEP, epigenomix, epivizr, exomeCopy, fastseg, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, GenomicFiles, genoset, ggtut, gmapR, GOTHiC, Gviz, hiAnnotator, HiTC, htSeqTools, intansv, methyAnalysis, minfi, MMDiff, OmicCircos, parathyroidSE, PING, QuasR, r3Cseq, R453Plus1Toolbox, Rcade, rfPred, riboSeq, RIPSeeker, Rsamtools, rSFFreader, RSVSim, rtracklayer, segmentSeq, seqbias, SigFuge, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, trackViewer, TransView, VariantAnnotation, VariantTools, vtpnet, wavClusteR
Imports Me AnnotationHub, ArrayExpressHTS, beadarray, BEAT, biovizBase, BiSeq, BSgenome, CAGEr, CexoR, chipenrich,, ChIPseeker, chipseq, ChIPseqR, CNEr, copynumber, COSMIC.67, CoverageView, customProDB, DNaseR, DOQTL, easyRNASeq, flipflop, FunciSNP, GenomicAlignments, ggbio, GGtools, gwascat, h5vc, HTSeqGenie, HTSFilter, leeBamViews, lumi, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MEDIPS, methyAnalysis, MethylSeekR, methylumi, MinimumDistance, MMDiff, NarrowPeaks, nucleR, oligoClasses, pepDat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19, PICS, prebs, Pviz, QuasR, Rariant, Repitools, rnaSeqMap, roar, rSFFreader, segmentSeq, SeqArray, SeqVarTools, ShortRead, SNPchip, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, SplicingGraphs, TFBSTools, triplex, VanillaICE, VariantFiltering, waveTiling
Suggests Me BeadArrayUseCases, BiocGenerics, BiocParallel, cummeRbund, GenomeInfoDb, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, QDNAseq, SeqGSEA

Package Downloads

Package Source GenomicRanges_1.17.26.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicRanges_1.17.26.tgz
Mac OS X 10.9 (Mavericks) GenomicRanges_1.17.26.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center