GenomicRanges

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges.

Representation and manipulation of genomic intervals


Bioconductor version: Development (3.20)

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: Patrick Aboyoun [aut], Hervé Pagès [aut, cre], Michael Lawrence [aut], Sonali Arora [ctb], Martin Morgan [ctb], Kayla Morrell [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Lori Shepherd [ctb], Dan Tenenbaum [ctb], Daniel van Twisk [ctb]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 HTML 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

Details

biocViews Annotation, Coverage, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.57.0
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, stats4, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.37.1), GenomeInfoDb(>= 1.15.2)
Imports utils, stats, XVector(>= 0.29.2)
System Requirements
URL https://bioconductor.org/packages/GenomicRanges
Bug Reports https://github.com/Bioconductor/GenomicRanges/issues
See More
Suggests Matrix, Biobase, AnnotationDbi, annotate, Biostrings(>= 2.25.3), SummarizedExperiment(>= 0.1.5), Rsamtools(>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle
Linking To S4Vectors, IRanges
Enhances
Depends On Me alabaster.ranges, AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, betaHMM, BindingSiteFinder, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, chromstaR, CINdex, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, Cogito, compEpiTools, consensusSeekeR, CSAR, csaw, CSSQ, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DNAshapeR, easylift, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, epigenomix, esATAC, EuPathDB, excluderanges, ExCluster, extraChIPs, fastseg, fCCAC, FindIT2, GeneBreak, geneRxCluster, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicPlot, GenomicScores, GenomicTuples, gmapR, gmoviz, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, HERON, hiAnnotator, HiCDOC, HiTC, IdeoViz, igvR, igvShiny, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, m6Aboost, maser, MBASED, Melissa, metagene2, methimpute, methodical, methylKit, methylPipe, minfi, MotifDb, motifTestR, msgbsR, MutationalPatterns, NADfinder, nullrangesData, OmicCircos, oncoscanR, ORFik, periodicDNA, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, ramr, recoup, regioneR, RepViz, rGREAT, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RNAmodR, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, SARC, Scale4C, SCOPE, segmentSeq, seqArchRplus, seqCAT, SeqGate, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SomaticSignatures, spiky, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, tadar, trackViewer, transmogR, TransView, traseR, tRNA, tRNAdbImport, tRNAscanImport, txdbmaker, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantTools, VplotR, vtpnet, vulcan, wavClusteR, WGSmapp, YAPSA
Imports Me ACE, alabaster.se, ALDEx2, amplican, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ASpli, AssessORF, ATACCoGAPS, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, ballgown, bambu, bamsignals, baySeq, BBCAnalyzer, beadarray, BEAT, BiFET, BiocOncoTK, BioMartGOGeneSets, BioPlex, BioTIP, biovizBase, biscuiteer, biscuiteerData, BiSeq, BOBaFIT, borealis, brainflowprobes, branchpointer, BREW3R.r, BRGenomics, BSgenomeForge, BUSpaRse, cageminer, CAGEr, cardelino, cBioPortalData, CexoR, cfdnakit, cfDNAPro, cfTools, ChAMP, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, ChromSCape, chromVAR, cicero, circRNAprofiler, cleanUpdTSeq, cliProfiler, CNEr, CNVfilteR, CNViz, CNVMetrics, comapr, coMET, coMethDMR, conumee, CopyNumberPlots, COSMIC.67, CoverageView, crisprBase, crisprBowtie, crisprDesign, CRISPRseek, CrispRVariants, crisprViz, CTexploreR, customProDB, DAMEfinder, Damsel, debrowser, decompTumor2Sig, deconvR, DEFormats, DegCre, DegNorm, deltaCaptureC, derfinder, derfinderPlot, DEWSeq, diffUTR, dinoR, DMRcate, DMRScan, dmrseq, DNAfusion, DominoEffect, doubletrouble, DRIMSeq, DropletUtils, easyRNASeq, EDASeq, EDIRquery, eisaR, ELMER, ELMER.data, enhancerHomologSearch, epialleleR, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epiregulon, epistack, EpiTxDb, epivizr, epivizrData, erma, EventPointer, ExpHunterSuite, factR, fcScan, FilterFFPE, fishpond, fitCons.UCSC.hg19, FLAMES, fourDNData, FRASER, GA4GHclient, gcapc, gDNAx, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicDistributionsData, GenomicInteractionNodes, GenomicInteractions, GenVisR, ggbio, gINTomics, GOfuncR, GrafGen, GRaNIE, gwascat, h5vc, heatmaps, hermes, HicAggR, HiCBricks, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, hicVennDiagram, HilbertCurve, HiLDA, hiReadsProcessor, HTSeqGenie, hummingbird, icetea, ideal, idr2d, IMAS, iNETgrate, InPAS, INSPEcT, ipdDb, IsoformSwitchAnalyzeR, isomiRs, IVAS, karyoploteR, katdetectr, knowYourCG, leeBamViews, loci2path, LOLA, LoomExperiment, lumi, MADSEQ, 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, magpie, mariner, mCSEA, mCSEAdata, MDTS, MEAL, MEDIPS, megadepth, memes, metaseqR2, methInheritSim, MethReg, methrix, methylCC, methylInheritance, MethylSeekR, MethylSeqData, methylSig, methylumi, MinimumDistance, MIRA, missMethyl, mitoClone2, MMDiff2, mobileRNA, Modstrings, monaLisa, Moonlight2R, mosaics, Motif2Site, motifbreakR, motifmatchr, MouseFM, MSA2dist, MultiAssayExperiment, multicrispr, MultiDataSet, multiHiCcompare, MungeSumstats, musicatk, NanoMethViz, nanotatoR, ncRNAtools, nearBynding, netDx, NoRCE, normr, nucleR, nullranges, OGRE, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, pageRank, panelcn.mops, partCNV, PAST, pcaExplorer, pepDat, pepStat, pgxRpi, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PhIPData, Pi, PICS, PING, PIPETS, plotgardener, plyinteractions, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, Pviz, QDNAseq, qpgraph, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, raer, RAIDS, RareVariantVis, RCAS, rCGH, RcisTarget, recount, recount3, recountWorkflow, regionalpcs, regioneR, regionReport, regutools, REMP, Repitools, RESOLVE, rfPred, rGADEM, RGMQL, RgnTX, Rhisat2, RiboCrypt, RiboDiPA, RiboProfiling, Rmmquant, rmspc, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, RTCGAToolbox, saseR, scanMiR, scanMiRApp, scDblFinder, scmeth, scMultiome, scoreInvHap, scPipe, scRNAseq, scRNAseqApp, scruff, scuttle, segmenter, seq2pathway, SeqArray, seqpac, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, shinyepico, ShortRead, signeR, SigsPack, SimFFPE, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, snapcount, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SOMNiBUS, SparseSignatures, spatialLIBD, spatzie, SpectralTAD, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, syntenet, systemPipeR, TAPseq, target, TCGAbiolinks, TCGAutils, TCGAWorkflow, TCseq, TDbasedUFE, TDbasedUFEadv, TENxIO, terraTCGAdata, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, tidybulk, tidyCoverage, TitanCNA, tLOH, tracktables, transcriptR, transite, TRESS, tricycle, triplex, TumourMethData, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, Uniquorn, UPDhmm, VariantFiltering, VariantToolsData, VaSP, VCFArray, wiggleplotr, xcore, XNAString, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, ZygosityPredictor
Suggests Me AlphaMissenseR, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, autonomics, BeadArrayUseCases, biobroom, BiocCheck, BiocGenerics, BiocParallel, CAGEWorkflow, Chicago, ComplexHeatmap, CTCF, cummeRbund, epivizrChart, GenomeInfoDb, GenomicState, GeuvadisTranscriptExpr, ggmanh, Glimma, GSReg, GWASTools, HDF5Array, InteractiveComplexHeatmap, interactiveDisplay, IRanges, lute, maftools, MetaScope, MiRaGE, MIRit, nanotubes, omicsPrint, parglms, recountmethylation, RNAmodR.Data, RTCGA, S4Vectors, SeqGSEA, shiny.gosling, Single.mTEC.Transcriptomes, splatter, systemPipeRdata, TFutils, universalmotif, updateObject, xcoredata
Links To Me
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Package Archives

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

Source Package GenomicRanges_1.57.0.tar.gz
Windows Binary GenomicRanges_1.57.0.zip
macOS Binary (x86_64) GenomicRanges_1.57.0.tgz
macOS Binary (arm64) GenomicRanges_1.57.0.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/
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