IRanges

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

Infrastructure for manipulating intervals on sequences

Installation

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

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

BiocManager::install("IRanges")

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("IRanges")

An Overview of the IRanges package	PDF	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	2.14.12
In Bioconductor since	BioC 2.3 (R-2.8) (15.5 years)
License	Artistic-2.0
Depends	R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.25.3), S4Vectors(>= 0.18.2)
Imports	stats4
System Requirements
URL

See More

Suggests	XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle
Linking To	S4Vectors
Enhances
Depends On Me	AnnotationDbi, AnnotationHubData, BaalChIP, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, CNPBayes, CODEX, consensusSeekeR, CSAR, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCHMM, DMRcaller, epigenomix, exomeCopy, fCCAC, FunciSNP.data, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, groHMM, gtrellis, Guitar, Gviz, harbChIP, HelloRanges, HilbertCurve, HiTC, HMMcopy, htSeqTools, IdeoViz, InTAD, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, NADfinder, ORFik, OTUbase, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, pepStat, PGA, PING, plyranges, proBAMr, PSICQUIC, RefNet, rfPred, rGADEM, rGREAT, RIPSeeker, RJMCMCNucleosomes, rMAT, Scale4C, scsR, SGSeq, SICtools, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, TEQC, traseR, triform, triplex, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XVector
Imports Me	ALDEx2, AllelicImbalance, alpine, amplican, AneuFinder, annmap, annotatr, ArrayExpressHTS, ArrayTV, ASpli, ATACseqQC, ballgown, bamsignals, BasicSTARRseq, BayesPeak, BBCAnalyzer, beadarray, biovizBase, BiSeq, BitSeq, bnbc, BPRMeth, branchpointer, BSgenome, bsseq, BUMHMM, CAGEfightR, CAGEr, cgdv17, CHARGE, charm, ChIC, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPSeqSpike, ChIPsim, ChromHeatMap, chromstaR, chromswitch, chromVAR, CINdex, cleaver, cn.mops, CNEr, CNVPanelizer, CNVrd2, cobindR, coMET, compEpiTools, contiBAIT, conumee, copynumber, CopywriteR, CoverageView, CRISPRseek, CrispRVariants, csaw, dada2, debrowser, DECIPHER, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DEScan2, DiffBind, diffHic, diffloop, DMRcate, DMRScan, dmrseq, DominoEffect, DOQTL, DRIMSeq, easyRNASeq, EDASeq, ELMER, EnrichedHeatmap, ensembldb, epivizr, epivizrData, erma, esATAC, facopy, fastseg, FindMyFriends, fitCons.UCSC.hg19, flipflop, flowQ, FunciSNP, GA4GHclient, gcapc, GDSArray, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractions, GenomicScores, GenomicTuples, genoset, genotypeeval, GenVisR, GGBase, ggbio, GGtools, girafe, gmapR, GoogleGenomics, GOpro, GOTHiC, gQTLstats, GUIDEseq, gwascat, h5vc, HDF5Array, heatmaps, HiCcompare, HTSeqGenie, ideal, IMAS, InPAS, INSPEcT, intansv, InteractionSet, IntEREst, InterMineR, IsoformSwitchAnalyzeR, isomiRs, IVAS, IWTomics, JunctionSeq, karyoploteR, LOLA, 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, MatrixRider, mCSEA, MDTS, MEAL, MEDIPS, metagene, methimpute, methInheritSim, methVisual, methyAnalysis, methylInheritance, methylKit, methylPipe, MethylSeekR, methylumi, methyvim, minfi, MinimumDistance, MIRA, mosaics, motifbreakR, motifmatchr, motifRG, MotIV, msa, msgbsR, MSnbase, MultiAssayExperiment, MultiDataSet, MutationalPatterns, NarrowPeaks, normr, nucleoSim, nucleR, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, panelcn.mops, Pbase, pcaExplorer, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.atdschip.tiling, pd.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, pdInfoBuilder, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PICS, PING, plethy, podkat, polyester, pqsfinder, prebs, PureCN, Pviz, QDNAseq, qpgraph, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, Rariant, Rcade, rCGH, recount, REDseq, regioneR, REMP, Repitools, ReportingTools, rGADEM, RiboProfiling, riboSeqR, rMAT, RNAprobR, rnaSeqMap, RnBeads, roar, Rqc, Rsamtools, rSFFreader, RSVSim, RTCGAToolbox, RTN, rtracklayer, SCAN.UPC, segmentSeq, SeqArray, seqCAT, seqPattern, seqplots, seqsetvis, SeqSQC, SeqVarTools, sevenC, ShortRead, simulatorZ, SMITE, SNPchip, SNPhood, 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, SomaticSignatures, SparseSignatures, spliceR, spliceSites, SplicingGraphs, SPLINTER, srnadiff, STAN, SummarizedExperiment, SVM2CRM, TarSeqQC, TCGAbiolinks, TCGAutils, TCseq, TFBSTools, TFEA.ChIP, TFHAZ, TFutils, TitanCNA, TnT, tracktables, trackViewer, transcriptR, TransView, triform, TSRchitect, TSSi, TVTB, TxRegInfra, Uniquorn, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, waveTiling, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss
Suggests Me	annotate, AnnotationHub, BaseSpaceR, BiocGenerics, Chicago, ClassifyR, epivizrChart, Glimma, gQTLBase, GWASTools, HilbertVis, HilbertVisGUI, martini, MiRaGE, regionReport, RTCGA, S4Vectors, yeastRNASeq
Links To Me	Biostrings, CNEr, DECIPHER, GenomicAlignments, GenomicRanges, kebabs, MatrixRider, Rsamtools, rSFFreader, rtracklayer, ShortRead, triplex, VariantAnnotation, VariantFiltering, XVector
Build Report	Build Report

Package Archives

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

Source Package	IRanges_2.14.12.tar.gz
Windows Binary	IRanges_2.14.12.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	IRanges_2.14.12.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IRanges
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IRanges
Bioc Package Browser	https://code.bioconductor.org/browse/IRanges/
Package Short Url	https://bioconductor.org/packages/IRanges/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive