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IRanges

This is thereleased version of IRanges; for the devel version, seeIRanges.

Foundation of integer range manipulation in Bioconductor

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DOI: 10.18129/B9.bioc.IRanges


Bioconductor version: Release (3.22)

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, entercitation("IRanges")):

Installation

To install this package, start R (version "4.5") and enter:

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

For older versions of R, please refer to the appropriateBioconductor 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 packagePDFR Script
Reference ManualPDF
NEWSText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsDataRepresentation,Infrastructure,Software
Version2.44.0
In Bioconductor sinceBioC 2.3 (R-2.8) (17 years)
LicenseArtistic-2.0
DependsR (>= 4.0.0), methods, utils, stats,BiocGenerics(>= 0.53.2),S4Vectors(>= 0.47.6)
Importsstats4
System Requirements
URLhttps://bioconductor.org/packages/IRanges
Bug Reportshttps://github.com/Bioconductor/IRanges/issues
See More
SuggestsXVector,GenomicRanges,Rsamtools,GenomicAlignments,GenomicFeatures,BSgenome.Celegans.UCSC.ce2,pasillaBamSubset,RUnit,BiocStyle
Linking ToS4Vectors
Enhances
Depends On MeAnnotationDbi,AnnotationHubData,BaalChIP,bambu,biomvRCNS,Biostrings,BiSeq,BSgenome,BSgenomeForge,bumphunter,CAFE,casper,CexoR,chimeraviz,ChIPpeakAnno,chipseq,cigarillo,CODEX,consensusSeekeR,CSAR,CSSQ,deepSNV,DelayedArray,DESeq2,DEXSeq,DirichletMultinomial,DMCFB,DMCHMM,DMRcaller,ExCluster,fCCAC,GenomeInfoDb,GenomicAlignments,GenomicDistributions,GenomicFeatures,GenomicRanges,groHMM,gtrellis,Gviz,HelloRanges,HERON,HiTC,IdeoViz,InTAD,MotifDb,MultimodalExperiment,NADfinder,oncoscanR,ORFik,OTUbase,pepStat,periodicDNA,plyranges,proBAMr,pwalign,rGREAT,RJMCMCNucleosomes,RNAmodR,S4Arrays,Scale4C,SCOPE,SGSeq,SICtools,Structstrings,TEQC,traseR,triplex,VariantTools,VplotR,XVector,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 Mealabaster.bumpy,alabaster.ranges,alabaster.se,ALDEx2,AllelicImbalance,amplican,annmap,annotatr,appreci8R,ASpli,AssessORF,ATACseqQC,ATACseqTFEA,atena,ballgown,bamsignals,BBCAnalyzer,BgeeCall,BindingSiteFinder,Bioc.gff,biovizBase,biscuiteer,BiSeq,bnbc,breakpointR,bsseq,BUMHMM,BumpyMatrix,BUSpaRse,CAGEfightR,cageminer,CAGEr,cBioPortalData,cfdnakit,cfDNAPro,ChIPanalyser,chipenrich,ChIPexoQual,ChIPseeker,chipseq,ChIPseqR,ChIPsim,ChromHeatMap,ChromSCape,chromVAR,cicero,circRNAprofiler,CircSeqAlignTk,cleanUpdTSeq,cleaver,cn.mops,CNEr,CNVfilteR,CNVMetrics,CNVPanelizer,CNVRanger,CNVrd2,COCOA,coMethDMR,compEpiTools,ComplexHeatmap,CompoundDb,conumee,CopyNumberPlots,CoverageView,crisprBase,crisprBowtie,crisprDesign,crisprScore,CRISPRseek,CrispRVariants,crisprViz,crupR,csaw,CTexploreR,dada2,DAMEfinder,debrowser,DECIPHER,deconvR,DegCre,DegNorm,DelayedMatrixStats,deltaCaptureC,demuxSNP,derfinder,derfinderHelper,derfinderPlot,DEScan2,DiffBind,diffHic,diffUTR,DMRcaller,DMRcate,DMRScan,dmrseq,DNAfusion,DominoEffect,dreamlet,DRIMSeq,DropletUtils,dStruct,easyRNASeq,EDASeq,eisaR,ELMER,ELViS,enhancerHomologSearch,EnrichedHeatmap,ensembldb,EpiCompare,epidecodeR,epigraHMM,EpiMix,epimutacions,epiregulon,epistack,EpiTxDb,epivizr,epivizrData,esATAC,EventPointer,extraChIPs,FastqCleaner,fastseg,fcScan,FilterFFPE,FindIT2,fishpond,FLAMES,FRASER,G4SNVHunter,GA4GHclient,gcapc,gDNAx,geneAttribution,GENESIS,genomation,GenomAutomorphism,genomeIntervals,GenomicAlignments,GenomicDataCommons,GenomicFiles,GenomicInteractionNodes,GenomicInteractions,GenomicOZone,GenomicPlot,GenomicScores,GenomicTuples,geomeTriD,ggbio,gmapR,gmoviz,GOfuncR,GOpro,GOTHiC,GSVA,GUIDEseq,gVenn,gwascat,h5mread,h5vc,HDF5Array,heatmaps,hermes,HicAggR,HiCaptuRe,HiCBricks,HiCcompare,HiCExperiment,HiContacts,hicVennDiagram,HilbertCurve,hummingbird,icetea,ideal,idr2d,igblastr,InPAS,INSPEcT,intansv,InteractionSet,InteractiveComplexHeatmap,IntEREst,ipdDb,iSEEu,IsoformSwitchAnalyzeR,IVAS,karyoploteR,katdetectr,knowYourCG,linkSet,LOLA,m6Aboost,magpie,mariner,maser,MatrixRider,mCSEA,MDTS,MEAL,MEDIPS,MesKit,metagene2,metaseqR2,methimpute,methInheritSim,methodical,MethReg,methrix,methylCC,methylInheritance,methylKit,methylPipe,MethylSeekR,methylSig,methylumi,mia,minfi,MinimumDistance,MIRA,missMethyl,mobileRNA,Modstrings,monaLisa,mosaics,MOSim,Motif2Site,motifbreakR,motifmatchr,MotifPeeker,motifTestR,MouseFM,msa,MSA2dist,MsBackendMassbank,MsBackendMgf,MsBackendMsp,MsBackendRawFileReader,MsBackendSql,MsExperiment,msgbsR,MSnbase,MultiAssayExperiment,MultiDataSet,mumosa,MungeSumstats,musicatk,MutationalPatterns,mutscan,NanoMethViz,NanoStringNCTools,ncRNAtools,normr,nucleoSim,nucleR,nullranges,OGRE,oligoClasses,OmaDB,OMICsPCA,openPrimeR,Organism.dplyr,OrganismDbi,OUTRIDER,OutSplice,packFinder,panelcn.mops,pcaExplorer,pdInfoBuilder,peakCombiner,PhIPData,PICB,plotgardener,plyinteractions,podkat,pqsfinder,pram,prebs,preciseTAD,primirTSS,proActiv,ProteoDisco,PSMatch,PureCN,Pviz,QDNAseq,QFeatures,qpgraph,qPLEXanalyzer,qsea,QuasR,R3CPET,r3Cseq,raer,RaggedExperiment,RAIDS,ramr,RareVariantVis,RCAS,recount,recoup,REDseq,regioneR,regutools,REMP,ReportingTools,RESOLVE,rfaRm,rfPred,RgnTX,RiboCrypt,RiboDiPA,RiboProfiling,riboSeqR,ribosomeProfilingQC,rigvf,rnaEditr,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,RnBeads,roar,rprimer,Rqc,Rsamtools,RSVSim,RTN,rtracklayer,sarks,saseR,SCAN.UPC,scanMiR,scanMiRApp,scDblFinder,scHOT,scPipe,scRNAseqApp,segmenter,segmentSeq,SeqArray,seqCAT,Seqinfo,seqPattern,seqsetvis,SeqSQC,SeqVarTools,sesame,sevenC,ShortRead,signeR,signifinder,SimFFPE,SingleMoleculeFootprinting,sitadela,Site2Target,SMITE,snapcount,SNPhood,SomaticSignatures,SOMNiBUS,SparseArray,SparseSignatures,Spectra,SpectriPy,spiky,SpliceWiz,SplicingGraphs,SPLINTER,srnadiff,STADyUM,strandCheckR,StructuralVariantAnnotation,SummarizedExperiment,SynExtend,tadar,TAPseq,target,TCGAbiolinks,TCGAutils,TCseq,TENET,TFBSTools,TFEA.ChIP,TFHAZ,tidyCoverage,TnT,tracktables,trackViewer,transcriptR,transmogR,TreeSummarizedExperiment,TRESS,tricycle,tRNA,tRNAdbImport,tRNAscanImport,TVTB,txcutr,txdbmaker,tximeta,UMI4Cats,Uniquorn,universalmotif,UPDhmm,VanillaICE,VarCon,VariantAnnotation,VariantExperiment,VariantFiltering,VaSP,VDJdive,vmrseq,wavClusteR,wiggleplotr,xcms,xcore,XVector,yamss,ZygosityPredictor,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,cpp11bigwig,crispRdesignR,cubar,GencoDymo2,geno2proteo,GenoPop,hahmmr,HiCociety,hoardeR,ICAMS,iimi,karyotapR,locuszoomr,longreadvqs,LoopRig,MAAPER,MitoHEAR,noisyr,numbat,PACVr,refseqR,revert,rnaCrosslinkOO,SATS,Signac,tidygenomics,VALERIE
Suggests Meannotate,AnnotationHub,BaseSpaceR,BiocGenerics,BREW3R.r,CCAFE,Chicago,ClassifyR,DFplyr,easylift,epivizrChart,gDRcore,gDRutils,Glimma,GWASTools,HilbertVis,HilbertVisGUI,iscream,maftools,martini,MiRaGE,multicrispr,partCNV,plyxp,regionReport,RTCGA,S4Vectors,SigsPack,splatter,svaNUMT,svaRetro,systemPipeR,TFutils,tidybulk,MetaScope,scMultiome,systemPipeRdata,xcoredata,yeastRNASeq,fuzzyjoin,gggenomes,gkmSVM,MiscMetabar,MoBPS,polyRAD,pQTLdata,rliger,scPloidy,seqmagick,Seurat,sigminer,SNPassoc,updog,valr
Links To MeBioc.gff,Biostrings,cigarillo,CNEr,DECIPHER,GenomicAlignments,GenomicRanges,kebabs,MatrixRider,pwalign,Rsamtools,rtracklayer,ShortRead,SparseArray,Structstrings,triplex,VariantAnnotation,VariantFiltering,XVector
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageIRanges_2.44.0.tar.gz
Windows Binary (x86_64) IRanges_2.44.0.zip
macOS Binary (x86_64)IRanges_2.44.0.tgz
macOS Binary (arm64)IRanges_2.44.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/IRanges
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/IRanges
Bioc Package Browserhttps://code.bioconductor.org/browse/IRanges/
Package Short Urlhttps://bioconductor.org/packages/IRanges/
Package Downloads ReportDownload Stats
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