IRanges

DOI: 10.18129/B9.bioc.IRanges    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see IRanges.

Infrastructure for manipulating intervals on sequences

Bioconductor version: 3.8

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: H. Pagès, P. Aboyoun and M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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 2.16.0
In Bioconductor since BioC 2.3 (R-2.8) (10.5 years)
License Artistic-2.0
Depends R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.25.3), S4Vectors(>= 0.19.11)
Imports stats4
LinkingTo S4Vectors
Suggests XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me AnnotationDbi, AnnotationHubData, BaalChIP, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, chroGPS, CNPBayes, CODEX, consensusSeekeR, CSAR, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCHMM, DMRcaller, epigenomix, ExCluster, exomeCopy, fCCAC, FunciSNP.data, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, groHMM, gtrellis, Guitar, Gviz, harbChIP, HelloRanges, HiTC, HMMcopy, htSeqTools, IdeoViz, InTAD, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, NADfinder, 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, PGA, PING, plyranges, proBAMr, PSICQUIC, RefNet, rfPred, rGADEM, rGREAT, RIPSeeker, RJMCMCNucleosomes, rMAT, Scale4C, scsR, SGSeq, SICtools, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, TEQC, traseR, triform, triplex, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XVector
Imports Me ALDEx2, AllelicImbalance, alpine, amplican, AneuFinder, annmap, annotatr, appreci8R, ArrayExpressHTS, ArrayTV, ASpli, AssessORF, ATACseqQC, ballgown, bamsignals, BasicSTARRseq, BayesPeak, BBCAnalyzer, beadarray, BiocOncoTK, biovizBase, BiSeq, BitSeq, bnbc, BPRMeth, branchpointer, breakpointR, BSgenome, bsseq, BUMHMM, CAGEfightR, CAGEr, cgdv17, CHARGE, charm, ChIC, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPSeqSpike, ChIPsim, ChromHeatMap, chromstaR, chromswitch, chromVAR, cicero, CINdex, cleaver, cn.mops, CNEr, CNVPanelizer, CNVrd2, cobindR, COCOA, coMET, compEpiTools, contiBAIT, conumee, copynumber, CopywriteR, CoverageView, CRISPRseek, CrispRVariants, csaw, dada2, debrowser, DECIPHER, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DEScan2, DiffBind, diffHic, diffloop, DMRcate, DMRScan, dmrseq, DominoEffect, DOQTL, DRIMSeq, easyRNASeq, EDASeq, ELMER, EnrichedHeatmap, ensembldb, epivizr, epivizrData, erma, esATAC, EventPointer, facopy, FastqCleaner, fastseg, FindMyFriends, fitCons.UCSC.hg19, flipflop, flowQ, FunciSNP, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractions, GenomicScores, GenomicTuples, genoset, genotypeeval, GenVisR, GGBase, ggbio, GGtools, girafe, gmapR, GOfuncR, GoogleGenomics, GOpro, GOTHiC, gpart, gQTLstats, GUIDEseq, gwascat, h5vc, HDF5Array, heatmaps, HiCBricks, HiCcompare, HilbertCurve, HTSeqGenie, icetea, ideal, IMAS, InPAS, INSPEcT, intansv, InteractionSet, IntEREst, InterMineR, ipdDb, IsoformSwitchAnalyzeR, isomiRs, IVAS, IWTomics, JunctionSeq, karyoploteR, LOLA, M3D, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.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.r2.0.1.GRCh38, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, maser, MatrixRider, mCSEA, MDTS, MEAL, MEDIPS, metagene, methimpute, methInheritSim, methVisual, methyAnalysis, methylInheritance, methylKit, methylPipe, MethylSeekR, methylumi, methyvim, minfi, MinimumDistance, MIRA, mosaics, motifbreakR, motifmatchr, motifRG, MotIV, msa, msgbsR, MSnbase, MTseeker, MTseekerData, MultiAssayExperiment, MultiDataSet, MutationalPatterns, NarrowPeaks, normr, nucleoSim, nucleR, oligoClasses, OmaDB, OMICsPCA, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, panelcn.mops, Pbase, 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, PICS, PING, plethy, podkat, polyester, pqsfinder, prebs, primirTSS, PureCN, Pviz, QDNAseq, qpgraph, qPLEXanalyzer, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, Rariant, Rcade, rCGH, recount, REDseq, regioneR, REMP, Repitools, ReportingTools, rGADEM, RiboProfiling, riboSeqR, rMAT, RNAprobR, rnaSeqMap, RnBeads, roar, Rqc, Rsamtools, rSFFreader, RSVSim, RTCGAToolbox, RTN, rtracklayer, SCAN.UPC, segmentSeq, SeqArray, seqCAT, seqPattern, seqplots, seqsetvis, SeqSQC, SeqVarTools, sesame, sevenC, ShortRead, SMITE, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticCancerAlterations, SomaticSignatures, SparseSignatures, spliceSites, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, SummarizedExperiment, SVM2CRM, TarSeqQC, TCGAbiolinks, TCGAutils, TCseq, TFBSTools, TFEA.ChIP, TFHAZ, TitanCNA, TnT, tracktables, trackViewer, transcriptR, TransView, triform, tRNA, tRNAdbImport, TSRchitect, TSSi, TVTB, TxRegInfra, Uniquorn, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, waveTiling, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss
Suggests Me annotate, AnnotationHub, BaseSpaceR, BiocGenerics, Chicago, ClassifyR, epivizrChart, Glimma, gQTLBase, GWASTools, HilbertVis, HilbertVisGUI, martini, MiRaGE, regionReport, RTCGA, S4Vectors, TFutils, yeastRNASeq
Links To Me Biostrings, CNEr, DECIPHER, GenomicAlignments, GenomicRanges, kebabs, MatrixRider, Rsamtools, rSFFreader, rtracklayer, ShortRead, triplex, VariantAnnotation, VariantFiltering, XVector
Build Report  

Package Archives

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

Source Package IRanges_2.16.0.tar.gz
Windows Binary IRanges_2.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) IRanges_2.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/IRanges
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IRanges
Package Short Url http://bioconductor.org/packages/IRanges/
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