IRanges

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see IRanges.

Foundation of integer range manipulation in Bioconductor

Installation

To install this package, start R (version "4.4") 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	2.38.1
In Bioconductor since	BioC 2.3 (R-2.8) (16 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, utils, stats, BiocGenerics(>= 0.39.2), S4Vectors(>= 0.33.3)
Imports	stats4
System Requirements
URL	https://bioconductor.org/packages/IRanges
Bug Reports	https://github.com/Bioconductor/IRanges/issues

See More

Suggests	XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle
Linking To	S4Vectors
Enhances
Depends On Me	AnnotationDbi, AnnotationHubData, BSgenomeForge, BSgenome, BaalChIP, BiSeq, Biostrings, BubbleTree, CAFE, CODEX, CSAR, CSSQ, CexoR, ChIPpeakAnno, DESeq2, DEXSeq, DMCFB, DMCHMM, DMRcaller, DelayedArray, DirichletMultinomial, ExCluster, GenomeInfoDb, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicRanges, Gviz, HERON, HelloRanges, HiTC, IdeoViz, InTAD, MotifDb, MultimodalExperiment, NADfinder, ORFik, OTUbase, RJMCMCNucleosomes, RNAmodR, RepViz, S4Arrays, SCOPE, SGSeq, SICtools, Scale4C, Structstrings, TEQC, VariantTools, VplotR, XVector, bambu, biomvRCNS, bumphunter, casper, chimeraviz, chipseq, consensusSeekeR, customProDB, deepSNV, epigenomix, fCCAC, groHMM, gtrellis, oncoscanR, pepStat, periodicDNA, plyranges, proBAMr, pwalign, rGADEM, rGREAT, seqArchRplus, traseR, triplex, 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, harbChIP, LiebermanAidenHiC2009
Imports Me	ALDEx2, ASpli, ATACCoGAPS, ATACseqQC, ATACseqTFEA, AllelicImbalance, AneuFinder, AssessORF, BBCAnalyzer, BPRMeth, BUMHMM, BUSpaRse, BiSeq, BindingSiteFinder, BiocOncoTK, BumpyMatrix, CAGEfightR, CAGEr, CINdex, CNEr, CNVMetrics, CNVPanelizer, CNVRanger, CNVfilteR, CNVrd2, COCOA, CRISPRseek, CTexploreR, ChIPQC, ChIPanalyser, ChIPexoQual, ChIPseeker, ChIPseqR, ChIPsim, ChromHeatMap, ChromSCape, CircSeqAlignTk, ComplexHeatmap, CompoundDb, CopyNumberPlots, CoverageView, CrispRVariants, DAMEfinder, DECIPHER, DEScan2, DMRScan, DMRcate, DNAfusion, DRIMSeq, DegCre, DegNorm, DelayedMatrixStats, DiffBind, DominoEffect, DropletUtils, EDASeq, ELMER, EnrichedHeatmap, EpiMix, EpiTxDb, EventPointer, FLAMES, FRASER, FastqCleaner, FilterFFPE, FindIT2, GA4GHclient, GENESIS, GOTHiC, GOfuncR, GOpro, GSVA, GUIDEseq, GenVisR, GeneGeneInteR, GenomAutomorphism, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenomicTuples, HDF5Array, HTSeqGenie, HiCBricks, HiCExperiment, HiCcompare, HiContacts, HiCool, HicAggR, HilbertCurve, IMAS, INSPEcT, IVAS, InPAS, IntEREst, InterMineR, InteractionSet, InteractiveComplexHeatmap, IsoformSwitchAnalyzeR, LOLA, LinTInd, MADSEQ, MDTS, MEAL, MEDIPS, MIRA, MOSim, MSA2dist, MSnbase, MatrixRider, MesKit, MethReg, MethylSeekR, MinimumDistance, Modstrings, Motif2Site, MouseFM, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsExperiment, MultiAssayExperiment, MultiDataSet, MungeSumstats, MutationalPatterns, NanoMethViz, NanoStringNCTools, OGRE, OMICsPCA, OUTRIDER, OmaDB, Organism.dplyr, OrganismDbi, OutSplice, PICS, PING, PhIPData, ProteoDisco, PureCN, Pviz, QDNAseq, QFeatures, QuasR, R3CPET, R453Plus1Toolbox, RAIDS, RCAS, REDseq, REMP, RESOLVE, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RSVSim, RTN, RaggedExperiment, RareVariantVis, Repitools, ReportingTools, RgnTX, RiboCrypt, RiboDiPA, RiboProfiling, RnBeads, Rqc, Rsamtools, SARC, SCAN.UPC, SMITE, SNPhood, SOMNiBUS, SPLINTER, SeqArray, SeqSQC, SeqVarTools, ShortRead, SimFFPE, SingleMoleculeFootprinting, SomaticSignatures, SparseArray, SparseSignatures, Spectra, SpliceWiz, SplicingGraphs, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, TAPseq, TCGAbiolinks, TCGAutils, TCseq, TFBSTools, TFEA.ChIP, TFHAZ, TRESS, TVTB, TitanCNA, TnT, TransView, TreeSummarizedExperiment, UMI4Cats, UPDhmm, Uniquorn, VDJdive, VaSP, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantFiltering, XNAString, XVector, ZygosityPredictor, alabaster.bumpy, alabaster.ranges, alabaster.se, amplican, annmap, annotatr, appreci8R, atena, ballgown, bamsignals, beadarray, biovizBase, biscuiteer, bnbc, branchpointer, breakpointR, bsseq, cBioPortalData, cageminer, cfDNAPro, cfdnakit, chipenrich, chipseq, chromVAR, chromstaR, cicero, circRNAprofiler, cleanUpdTSeq, cleaver, cn.mops, coMethDMR, comapr, compEpiTools, conumee, crisprBase, crisprBowtie, crisprDesign, crisprScore, crisprViz, csaw, dStruct, dada2, debrowser, deconvR, deltaCaptureC, demuxSNP, derfinderHelper, derfinderPlot, derfinder, diffHic, diffUTR, dmrseq, dreamlet, easyRNASeq, eisaR, enhancerHomologSearch, ensembldb, epidecodeR, epigraHMM, epimutacions, epiregulon, epistack, epivizrData, epivizr, erma, esATAC, extraChIPs, factR, fastseg, fcScan, fishpond, gDNAx, gcapc, geneAttribution, genomation, genomeIntervals, ggbio, girafe, gmapR, gmoviz, gwascat, h5vc, heatmaps, hermes, hicVennDiagram, hummingbird, iSEEu, icetea, ideal, idr2d, intansv, ipdDb, isomiRs, karyoploteR, katdetectr, knowYourCG, m6Aboost, mCSEA, magpie, mariner, maser, metagene2, metaseqR2, methInheritSim, methimpute, methodical, methrix, methylCC, methylInheritance, methylKit, methylPipe, methylSig, methylumi, mia, microbiomeMarker, minfi, missMethyl, mobileRNA, monaLisa, mosaics, motifTestR, motifbreakR, motifmatchr, msa, msgbsR, mumosa, musicatk, ncRNAtools, normr, nucleR, nucleoSim, nullranges, oligoClasses, openPrimeR, packFinder, panelcn.mops, pcaExplorer, pdInfoBuilder, plotgardener, plyinteractions, podkat, polyester, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, profileplyr, qPLEXanalyzer, qpgraph, qsea, r3Cseq, raer, ramr, recount, recoup, regioneR, regutools, rfPred, rfaRm, riboSeqR, ribosomeProfilingQC, rnaEditr, roar, rprimer, rtracklayer, sarks, saseR, scDblFinder, scHOT, scPipe, scRNAseqApp, scanMiRApp, scanMiR, segmentSeq, segmenter, seqCAT, seqPattern, seqsetvis, sesame, sevenC, signeR, signifinder, sitadela, snapcount, soGGi, spatzie, spiky, srnadiff, strandCheckR, tRNA, tRNAdbImport, tRNAscanImport, tadar, target, tidyCoverage, trackViewer, tracktables, transcriptR, transmogR, tricycle, txcutr, txdbmaker, tximeta, universalmotif, wavClusteR, wiggleplotr, xcms, xcore, yamss, fitCons.UCSC.hg19, GenomicState, 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.v3.1.2.GRCh38, MafH5.gnomAD.v4.0.GRCh38, 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.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, chipenrich.data, fourDNData, leeBamViews, MethylSeqData, pd.atdschip.tiling, sesameData, SomaticCancerAlterations, spatialLIBD, seqpac, alakazam, crispRdesignR, cubar, geneHapR, geno2proteo, GenoPop, hahmmr, hoardeR, ICAMS, iimi, karyotapR, locuszoomr, lolliplot, longreadvqs, LoopRig, MAAPER, MitoHEAR, MOCHA, noisyr, numbat, oncoPredict, PACVr, RapidoPGS, refseqR, revert, rnaCrosslinkOO, RTIGER, Signac, simMP, STRMPS, tidygenomics, VALERIE
Suggests Me	AnnotationHub, BREW3R.r, BaseSpaceR, BiocGenerics, Chicago, ClassifyR, GWASTools, Glimma, HilbertVisGUI, HilbertVis, MiRaGE, RTCGA, S4Vectors, SigsPack, TFutils, annotate, easylift, epivizrChart, gDRcore, gDRutils, maftools, martini, multicrispr, partCNV, regionReport, regionalpcs, splatter, svaNUMT, svaRetro, systemPipeR, tidybulk, MetaScope, scMultiome, systemPipeRdata, xcoredata, yeastRNASeq, fuzzyjoin, gkmSVM, MARVEL, polyRAD, rliger, scPloidy, seqmagick, Seurat, sigminer, SNPassoc, updog, valr
Links To Me	Biostrings, CNEr, DECIPHER, GenomicAlignments, GenomicRanges, MatrixRider, Rsamtools, ShortRead, SparseArray, Structstrings, VariantAnnotation, VariantFiltering, XVector, kebabs, pwalign, rtracklayer, triplex
Build Report	Build Report

Package Archives

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

Source Package	IRanges_2.38.1.tar.gz
Windows Binary (x86_64)	IRanges_2.38.1.zip
macOS Binary (x86_64)	IRanges_2.38.1.tgz
macOS Binary (arm64)	IRanges_2.38.1.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 3.19	Source Archive