IRanges

DOI: 10.18129/B9.bioc.IRanges  

Foundation of integer range manipulation in Bioconductor

Bioconductor version: Release (3.16)

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut]

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

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	2.32.0
In Bioconductor since	BioC 2.3 (R-2.8) (14.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, utils, stats, BiocGenerics(>= 0.39.2), S4Vectors(>= 0.33.3)
Imports	stats4
LinkingTo	S4Vectors
Suggests	XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/IRanges
BugReports	https://github.com/Bioconductor/IRanges/issues
Depends On Me	AnnotationDbi, AnnotationHubData, BaalChIP, bambu, biomvRCNS, Biostrings, BiSeq, BSgenome, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, CODEX, consensusSeekeR, CSAR, CSSQ, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, epihet, ExCluster, exomeCopy, fCCAC, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicRanges, groHMM, gtrellis, Gviz, harbChIP, HelloRanges, HiTC, IdeoViz, InTAD, LiebermanAidenHiC2009, MotifDb, NADfinder, oncoscanR, 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, periodicDNA, plyranges, proBAMr, RepViz, rGADEM, rGREAT, RJMCMCNucleosomes, RNAmodR, Scale4C, SCOPE, SGSeq, SICtools, Structstrings, TEQC, traseR, triplex, VariantTools, VplotR, XVector
Imports Me	ALDEx2, AllelicImbalance, alpine, amplican, AneuFinder, annmap, annotatr, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, AssessORF, ATACCoGAPS, ATACseqQC, ATACseqTFEA, atena, ballgown, bamsignals, BasicSTARRseq, BBCAnalyzer, beadarray, BiocOncoTK, biovizBase, biscuiteer, BiSeq, BitSeq, bnbc, BPRMeth, branchpointer, breakpointR, BRGenomics, BSgenome, bsseq, BUMHMM, BumpyMatrix, BUSpaRse, CAGEfightR, cageminer, CAGEr, cBioPortalData, cfDNAPro, ChIC, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, ChromSCape, chromstaR, chromswitch, chromVAR, cicero, CINdex, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, cleaver, cn.mops, CNEr, CNVfilteR, CNVMetrics, CNVPanelizer, CNVRanger, CNVrd2, COCOA, comapr, coMET, coMethDMR, compEpiTools, ComplexHeatmap, CompoundDb, contiBAIT, conumee, copynumber, CopyNumberPlots, CopywriteR, CoverageView, crisprBase, crisprBowtie, crisprDesign, crisprScore, CRISPRseek, CrispRVariants, crisprViz, csaw, dada2, DAMEfinder, dasper, debrowser, DECIPHER, deconvR, DegNorm, DelayedMatrixStats, deltaCaptureC, derfinder, derfinderHelper, derfinderPlot, DEScan2, DiffBind, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DNAfusion, DominoEffect, dpeak, DRIMSeq, DropletUtils, dStruct, easyRNASeq, EDASeq, eisaR, ELMER, enhancerHomologSearch, ENmix, EnrichedHeatmap, enrichTF, ensembldb, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epistack, EpiTxDb, epivizr, epivizrData, erma, esATAC, EventPointer, exomePeak2, extraChIPs, factR, FastqCleaner, fastseg, fcScan, FilterFFPE, FindIT2, fishpond, fitCons.UCSC.hg19, FRASER, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicScores, GenomicState, GenomicTuples, genotypeeval, GenVisR, ggbio, girafe, gmapR, gmoviz, GOfuncR, GOpro, GOTHiC, gpart, GSVA, GUIDEseq, gwascat, h5vc, HDF5Array, heatmaps, hermes, HiCBricks, HiCcompare, HiCDCPlus, HiContacts, HilbertCurve, HTSeqGenie, hummingbird, icetea, ideal, idr2d, IMAS, InPAS, INSPEcT, intansv, InteractionSet, InteractiveComplexHeatmap, IntEREst, InterMineR, ipdDb, iSEEu, IsoformSwitchAnalyzeR, isomiRs, IVAS, IWTomics, karyoploteR, katdetectr, leeBamViews, LinTInd, LOLA, m6Aboost, MACPET, 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.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, maser, MatrixRider, mCSEA, MDTS, MEAL, MEDIPS, MesKit, metagene, metagene2, metaseqR2, MethCP, methimpute, methInheritSim, MethReg, methrix, methylCC, methylInheritance, methylKit, methylPipe, MethylSeekR, MethylSeqData, methylSig, methylumi, mia, microbiomeMarker, minfi, MinimumDistance, MIRA, missMethyl, MMAPPR2, Modstrings, monaLisa, mosaics, MOSim, Motif2Site, motifbreakR, motifmatchr, MouseFM, msa, MSA2dist, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsExperiment, msgbsR, MSnbase, MultiAssayExperiment, MultiDataSet, mumosa, MungeSumstats, musicatk, MutationalPatterns, NanoStringNCTools, ncRNAtools, netDx, NoRCE, normr, nucleoSim, nucleR, nullranges, NxtIRFcore, ODER, OGRE, oligoClasses, OmaDB, OMICsPCA, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, packFinder, panelcn.mops, 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, PhIPData, Pi, PICS, PING, plethy, plotgardener, podkat, polyester, pqsfinder, pram, prebs, preciseTAD, PrecisionTrialDrawer, primirTSS, proActiv, profileplyr, ProteoDisco, PureCN, Pviz, QDNAseq, QFeatures, qpgraph, qPLEXanalyzer, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, RaggedExperiment, ramr, RareVariantVis, Rcade, RCAS, rCGH, recount, recoup, REDseq, regioneR, regutools, REMP, Repitools, ReportingTools, RESOLVE, rfaRm, rfPred, RgnTX, RiboCrypt, RiboDiPA, RiboProfiling, riboSeqR, ribosomeProfilingQC, RIPAT, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, roar, rprimer, Rqc, Rsamtools, RSVSim, RTN, rtracklayer, sarks, SCAN.UPC, scanMiR, scanMiRApp, SCANVIS, SCArray, scDblFinder, scHOT, scPipe, segmenter, segmentSeq, SeqArray, seqCAT, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, ShortRead, signeR, signifinder, SimFFPE, single, SingleMoleculeFootprinting, sitadela, SMITE, snapcount, SNPhood, 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, SomaticSignatures, SparseSignatures, spatialLIBD, spatzie, Spectra, spicyR, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, TAPseq, target, TarSeqQC, TCGAbiolinks, TCGAutils, TCseq, TFBSTools, TFEA.ChIP, TFHAZ, TitanCNA, TnT, tracktables, trackViewer, transcriptR, TransView, TreeSummarizedExperiment, TRESS, tricycle, tRNA, tRNAdbImport, tRNAscanImport, tscR, TVTB, txcutr, tximeta, UMI4Cats, Uniquorn, universalmotif, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantFiltering, VaSP, VDJdive, wavClusteR, wiggleplotr, XCIR, xcms, xcore, XNAString, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss
Suggests Me	annotate, AnnotationHub, BaseSpaceR, BiocGenerics, Chicago, ClassifyR, epivizrChart, Glimma, GWASTools, HilbertVis, HilbertVisGUI, maftools, martini, MiRaGE, multicrispr, regionReport, RTCGA, S4Vectors, SigsPack, splatter, svaNUMT, svaRetro, systemPipeR, systemPipeRdata, TFutils, xcoredata, yeastRNASeq
Links To Me	Biostrings, CNEr, DECIPHER, DegNorm, GenomicAlignments, GenomicRanges, kebabs, MatrixRider, Rsamtools, rtracklayer, ShortRead, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector
Build Report

Package Archives

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

Source Package	IRanges_2.32.0.tar.gz
Windows Binary	IRanges_2.32.0.zip
macOS Binary (x86_64)	IRanges_2.32.0.tgz
macOS Binary (arm64)	IRanges_2.32.0.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