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GenomicRanges

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

Representation and manipulation of genomic intervals and variables defined along a genome


Bioconductor version: 3.7

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

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

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.5") and enter: 


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicRanges")

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("GenomicRanges")
1. An Introduction to the GenomicRanges Package PDF R Script
2. GenomicRanges HOWTOs PDF R Script
3. A quick introduction to GRanges and GRangesList objects (slides) PDF R Script
4. Ten Things You Didn't Know (slides from BioC 2016) PDF R Script
5. Extending GenomicRanges PDF R Script
Reference Manual PDF
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.32.7
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License Artistic-2.0
Depends R (>= 2.10), methods, stats4, BiocGenerics(>= 0.25.3), S4Vectors(>= 0.17.32), IRanges(>= 2.14.4), GenomeInfoDb(>= 1.15.2)
Imports utils, stats, XVector(>= 0.19.8)
System Requirements
URL
See More
Suggests Biobase, AnnotationDbi(>= 1.21.1), annotate, Biostrings(>= 2.25.3), Rsamtools(>= 1.13.53), SummarizedExperiment(>= 0.1.5), Matrix, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, RNAseqData.HNRNPC.bam.chr14, hgu95av2probe
Linking To S4Vectors, IRanges
Enhances
Depends On Me AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, baySeq, biomvRCNS, BiSeq, bnbc, BPRMeth, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, CHARGE, cheung2010, chimera, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chroGPS, chromPlot, chromstaR, chromswitch, CINdex, cleanUpdTSeq, cn.mops, CNPBayes, cnvGSA, CNVPanelizer, compEpiTools, consensusSeekeR, CSAR, csaw, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCHMM, DMRcaller, DMRcatedata, DMRforPairs, DNAshapeR, DOQTL, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, esATAC, exomeCopy, fastseg, fCCAC, FourCSeq, FunChIP, GeneBreak, geneRxCluster, GenoGAM, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicScores, GenomicTuples, genoset, geuvStore2, gmapR, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, hiAnnotator, HilbertCurve, HiTC, htSeqTools, IdeoViz, igvR, InPAS, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, MBASED, metagene, methimpute, methyAnalysis, methylKit, methylPipe, minfi, msgbsR, MutationalPatterns, NADfinder, OmicCircos, ORFik, PGA, PING, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, Rariant, Rcade, recoup, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RJMCMCNucleosomes, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, segmentSeq, seqbias, seqCAT, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomaticSignatures, SummarizedExperiment, TarSeqQC, TnT, trackViewer, TransView, traseR, tRNAscanImport, VanillaICE, VariantAnnotation, VariantTools, vtpnet, vulcan, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, YAPSA
Imports Me ALDEx2, alpine, amplican, AnnotationFilter, annotatr, apeglm, ArrayExpressHTS, ASpli, ATACseqQC, BadRegionFinder, ballgown, bamsignals, BBCAnalyzer, beadarray, BEAT, BiFET, biovizBase, BiSeq, branchpointer, BSgenome, CAGEr, CexoR, cgdv17, ChAMP, ChIC, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, ChIPSeqSpike, chromDraw, ChromHeatMap, chromVAR, CNEr, coMET, contiBAIT, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, crisprseekplus, CrispRVariants, customProDB, DChIPRep, debrowser, DeepBlueR, DEFormats, derfinder, derfinderPlot, diffloop, DMRcate, DMRScan, dmrseq, DominoEffect, DRIMSeq, easyRNASeq, EDASeq, ELMER, ELMER.data, epivizr, epivizrData, erma, EventPointer, fitCons.UCSC.hg19, flipflop, FourCSeq, FunciSNP, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicInteractions, genotypeeval, GenVisR, GGBase, ggbio, GGtools, GOfuncR, GoogleGenomics, gQTLBase, gQTLstats, gwascat, h5vc, heatmaps, HiCcompare, hiReadsProcessor, HTSeqGenie, ideal, IMAS, INSPEcT, InterMineR, IsoformSwitchAnalyzeR, isomiRs, iteremoval, IVAS, JunctionSeq, karyoploteR, leeBamViews, loci2path, LOLA, lumi, M3D, 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, mCSEA, MDTS, MEAL, MEDIPS, methInheritSim, methyAnalysis, methylInheritance, MethylSeekR, methylumi, MinimumDistance, MIRA, MMDiff2, mosaics, motifbreakR, motifmatchr, MultiAssayExperiment, MultiDataSet, NarrowPeaks, normr, nucleR, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, panelcn.mops, Pbase, pcaExplorer, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, PICS, pqsfinder, prebs, proBAMr, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, qsea, R3CPET, R453Plus1Toolbox, RareVariantVis, RCAS, rCGH, recount, recountWorkflow, regioneR, regionReport, REMP, Repitools, RGMQL, RiboProfiling, RNAprobR, rnaSeqMap, roar, RTCGAToolbox, scmeth, scoreInvHap, seq2pathway, SeqArray, seqPattern, seqplots, seqsetvis, SeqSQC, SeqVarTools, sevenC, ShortRead, signeR, simulatorZ, SNPchip, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, 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, SomaticCancerAlterations, SparseSignatures, spliceR, SplicingGraphs, SPLINTER, srnadiff, STAN, SVM2CRM, systemPipeR, TCGAbiolinks, TCGAutils, TCGAWorkflow, TCseq, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, TFutils, TitanCNA, tracktables, transcriptR, trena, triplex, tRNAscanImport, TSRchitect, TVTB, TxRegInfra, Uniquorn, VariantFiltering, VariantToolsData, waveTiling, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, yriMulti
Suggests Me alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, Chicago, cummeRbund, epivizrChart, GenomeInfoDb, GeuvadisTranscriptExpr, Glimma, GSReg, GWASTools, HDF5Array, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, omicsPrint, Onassis, RTCGA, S4Vectors, SeqGSEA, Single.mTEC.Transcriptomes
Links To Me
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Package Archives

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

Source Package GenomicRanges_1.32.7.tar.gz
Windows Binary GenomicRanges_1.32.7.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GenomicRanges_1.32.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicRanges
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicRanges
Bioc Package Browser https://code.bioconductor.org/browse/GenomicRanges/
Package Short Url https://bioconductor.org/packages/GenomicRanges/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive