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Infrastructure for manipulating intervals on sequences

Bioconductor version: Release (3.2)

The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

Author: H. Pages, P. Aboyoun and M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at>

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PDF An Introduction to IRanges
PDF   Reference Manual
Text   NEWS


biocViews DataRepresentation, Infrastructure, Software
Version 2.4.4
In Bioconductor since BioC 2.3 (R-2.8) (7 years)
License Artistic-2.0
Depends R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.15.10), S4Vectors(>= 0.7.19)
Imports stats4
LinkingTo S4Vectors
Suggests XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit
Depends On Me AnnotationDbi, AnnotationHubData, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, casper, CexoR, ChIPComp, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, customProDB, DASiR, deepSNV, DESeq2, DEXSeq, DirichletMultinomial, DMRcaller, EnrichedHeatmap, epigenomix, exomeCopy,, geneRxCluster, GenomeInfoDb, genomes, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, groHMM, GUIDEseq, Guitar, Gviz, harbChIP, HilbertCurve, HiTC, HMMcopy, htSeqTools, IdeoViz, INSPEcT, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, oneChannelGUI, OTUbase,,,, pd.ath1.121501, pd.barley1,,, pd.bovine, pd.bsubtilis,,, pd.canine, pd.canine.2, pd.celegans, pd.chicken,,,,, pd.citrus, pd.cotton,,,,, pd.cytogenetics.array,,, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2,,,,,,,,, pd.genomewidesnp.5, pd.genomewidesnp.6,,, pd.hc.g110, pd.hg.focus,, 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.hta.2.0, pd.hu6800,,,,,, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240,,,,, pd.medicago,,,,,,, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b,,,,,, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177,,, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine,,,,, pd.rae230a, pd.rae230b,,,,,, pd.rat230.2,,, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c,,, pd.rhesus, pd.rice,,, pd.rn.u34, pd.rta.1.0,,, pd.s.aureus, pd.soybean,,, 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.zebrafish, pepStat, PGA, PING, proBAMr, PSICQUIC, RefNet, rfPred, rGADEM, rGREAT, RIPSeeker, rMAT, Rsamtools, scsR, segmentSeq, SGSeq, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomatiCA, TEQC, TitanCNA, traseR, triform, triplex, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XVector
Imports Me ALDEx2, AllelicImbalance, annmap, AnnotationDbi, ArrayExpressHTS, ballgown, bamsignals, BayesPeak, beadarray, Biostrings, biovizBase, BiSeq, BitSeq, BSgenome, CAGEr, cgdv17, ChAMP, charm, chipenrich,, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cleaver, CNEr, CNPBayes, CNVPanelizer, CNVrd2, cobindR, coMET, compEpiTools, conumee, copynumber, CopywriteR, CoverageView, csaw, customProDB, DECIPHER, derfinder, derfinderHelper, derfinderPlot, DiffBind, diffHic, DOQTL, easyRNASeq, EDASeq, ELMER, ensembldb, facopy, fastseg, FindMyFriends, flipflop, flowQ, FunciSNP, genomation, genomeIntervals, GenomicAlignments, GenomicFiles, GenomicInteractions, GenomicTuples, genoset, genotypeeval, GGBase, ggbio, GGtools, girafe, gmapR, GoogleGenomics, GOTHiC, gQTLstats, gwascat, h5vc, HTSeqGenie, InPAS, intansv, IVAS, LOLA, M3D, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, MatrixRider, MEAL, MEDIPS, metagene, methVisual, methyAnalysis, methylPipe, MethylSeekR, methylumi, minfi, MinimumDistance, MMDiff, mosaics, motifbreakR, motifRG, MotIV, msa, MSnbase, NarrowPeaks, nucleR, oligoClasses, OrganismDbi, Pbase, 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.mirna.3.1, pdInfoBuilder, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PICS, PING, plethy, podkat, polyester, prebs, Pviz, qpgraph, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, RareVariantVis, Rariant, rCGH, REDseq, regionReport, Repitools, ReportingTools, rGADEM, RiboProfiling, rMAT, rnaSeqMap, RnBeads, Rolexa, Rqc, rSFFreader, RSVSim, RTN, rtracklayer, SCAN.UPC, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, SICtools, simulatorZ, skewr, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, soGGi, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, SplicingGraphs, SummarizedExperiment, SVM2CRM, TarSeqQC, TCGAbiolinks, TFBSTools, tracktables, trackViewer, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, waveTiling, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Suggests Me AnnotationHub, BaseSpaceR, BiocGenerics, ClassifyR, gQTLBase, HilbertVis, HilbertVisGUI, MiRaGE, S4Vectors, STAN, yeastRNASeq
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