IRanges

This is the development version of IRanges; for the stable release version, see IRanges.

Foundation of integer range manipulation in Bioconductor

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	2.41.0
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

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, 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, 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, RgnTX, RiboCrypt, RiboDiPA, RiboProfiling, RnBeads, Rqc, Rsamtools, SARC, SCAN.UPC, SMITE, SNPhood, 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, 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, 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, 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, pdInfoBuilder, plotgardener, plyinteractions, podkat, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, profileplyr, 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, 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
Build Report	Build Report

Package Archives

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

Source Package	IRanges_2.41.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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