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IRanges

This is the released version of IRanges; for the devel version, see IRanges.

Foundation of integer range manipulation in Bioconductor


Bioconductor version: Release (3.20)

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>

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software
Version 2.40.0
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(>= 0.43.2)
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, gtrellis, oncoscanR, pepStat, periodicDNA, plyranges, proBAMr, pwalign, rGADEM, rGREAT, 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, ATACseqQC, ATACseqTFEA, AllelicImbalance, AneuFinder, AssessORF, BBCAnalyzer, BPRMeth, BUMHMM, BUSpaRse, BiSeq, BindingSiteFinder, 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, EpiCompare, 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, HiCBricks, HiCExperiment, HiCcompare, HiContacts, HiCool, HicAggR, HilbertCurve, IMAS, INSPEcT, IVAS, InPAS, IntEREst, InteractionSet, InteractiveComplexHeatmap, IsoformSwitchAnalyzeR, LOLA, LinTInd, MADSEQ, MDTS, MEAL, MEDIPS, MIRA, MOSim, MSA2dist, MSnbase, MatrixRider, MesKit, 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, SPLINTER, SeqArray, SeqSQC, SeqVarTools, ShortRead, SimFFPE, SomaticSignatures, SparseArray, SparseSignatures, Spectra, SpliceWiz, SplicingGraphs, StructuralVariantAnnotation, SummarizedExperiment, SynExtend, TAPseq, TCGAbiolinks, TCGAutils, TCseq, TFBSTools, TFEA.ChIP, TFHAZ, TRESS, TVTB, TitanCNA, TnT, 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, 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, geomeTriD, ggbio, girafe, gmapR, gmoviz, gwascat, h5vc, heatmaps, hermes, hicVennDiagram, hummingbird, iSEEu, icetea, ideal, idr2d, intansv, ipdDb, isomiRs, karyoploteR, katdetectr, knowYourCG, m6Aboost, magpie, mariner, maser, metagene2, metaseqR2, methInheritSim, methimpute, methrix, methylCC, methylInheritance, methylKit, methylPipe, methylSig, methylumi, mia, 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, 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, sitadela, snapcount, soGGi, spatzie, spiky, 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.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, DFplyr, GWASTools, Glimma, HilbertVisGUI, HilbertVis, MiRaGE, RTCGA, S4Vectors, SigsPack, TFutils, annotate, easylift, epivizrChart, gDRcore, gDRutils, maftools, martini, multicrispr, partCNV, plyxp, 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
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Package Archives

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

Source Package IRanges_2.40.0.tar.gz
Windows Binary (x86_64) IRanges_2.40.0.zip
macOS Binary (x86_64) IRanges_2.40.0.tgz
macOS Binary (arm64) IRanges_2.40.0.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/
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