IRanges

Infrastructure for manipulating intervals on sequences

Bioconductor version: Development (3.0)

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 bioconductor.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("IRanges")

To cite this package in a publication, start R and enter:

    citation("IRanges")

Documentation

PDF R Script An Introduction to IRanges
PDF R Script Rle Tips and Tricks
PDF   Reference Manual
Text   NEWS

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.99.0
In Bioconductor since BioC 2.3 (R-2.8)
License Artistic-2.0
Depends R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.9.1), S4Vectors
Imports methods, utils, stats, BiocGenerics, S4Vectors, stats4
Suggests XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit
System Requirements
URL
Depends On Me AnnotationHub, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, bsseq, bumphunter, CAFE, casper, CexoR, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, customProDB, DASiR, deepSNV, DESeq2, DEXSeq, DirichletMultinomial, DNaseR, epigenomix, exomeCopy, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, genoset, girafe, harbChIP, HiTC, HMMcopy, htSeqTools, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, nucleR, oneChannelGUI, PING, PSICQUIC, RefNet, rfPred, rGADEM, RIPSeeker, rMAT, Rsamtools, rSFFreader, scsR, segmentSeq, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SplicingGraphs, TEQC, triform, triplex, VariantTools, XVector
Imports Me AllelicImbalance, annmap, AnnotationDbi, ArrayExpressHTS, BayesPeak, beadarray, Biostrings, biovizBase, BiSeq, BitSeq, BSgenome, CAGEr, cgdv17, charm, chipenrich, chipenrich.data, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cleaver, cn.mops, CNEr, CNVrd2, cobindR, copynumber, CoverageView, customProDB, DECIPHER, DiffBind, easyRNASeq, EDASeq, fastseg, flipflop, flowQ, FunciSNP, gCMAPWeb, GenomicAlignments, GenomicRanges, ggbio, GGtools, girafe, gmapR, GOTHiC, Gviz, gwascat, h5vc, HTSeqGenie, HTSFilter, intansv, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MEDIPS, MeSHDbi, methVisual, methyAnalysis, MethylSeekR, minfi, MinimumDistance, MMDiff, mosaics, motifRG, MotIV, MSnbase, NarrowPeaks, nucleR, oligoClasses, OTUbase, 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.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.atdschip.tiling, 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.charm.hg18.example, pd.chicken, pd.citrus, 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.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, 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.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.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.3.1, 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.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.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.1.1.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.1.1.st, pd.rn.u34, pd.s.aureus, pd.soybean, 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, pdInfoBuilder, phastCons100way.UCSC.hg19, PICS, plethy, prebs, QuasR, R453Plus1Toolbox, Rariant, Rcade, REDseq, Repitools, ReportingTools, rGADEM, rMAT, rnaSeqMap, roar, Rolexa, rSFFreader, RSVSim, RTN, rtracklayer, segmentSeq, SeqArray, SeqVarTools, ShortRead, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, SplicingGraphs, TFBSTools, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantFiltering, waveTiling, XVector
Suggests Me BaseSpaceR, BiocGenerics, GenomeInfoDb, GenomicFiles, HilbertVis, HilbertVisGUI, MiRaGE, S4Vectors, SNPchip, yeastRNASeq

Package Downloads

Package Source IRanges_1.99.0.tar.gz
Windows Binary IRanges_1.99.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) IRanges_1.99.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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