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

IRanges

Infrastructure for manipulating intervals on sequences

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IRanges")

 

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	1.20.7
In Bioconductor since	BioC 2.3 (R-2.8)
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, utils, stats, BiocGenerics(>= 0.7.7)
Imports	methods, utils, stats, BiocGenerics, stats4
Suggests	XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit
System Requirements
URL
Depends On Me	AnnotationHub, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, bsseq, bumphunter, casper, CexoR, ChIPpeakAnno, chipseq, chroGPS, cn.mops, CSAR, customProDB, DASiR, DECIPHER, deepSNV, DESeq2, DirichletMultinomial, DNaseR, easyRNASeq, epigenomix, exomeCopy, genomes, GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools, girafe, gwascat, harbChIP, HiTC, HMMcopy, htSeqTools, LiebermanAidenHiC2009, methyAnalysis, MinimumDistance, MotifDb, motifRG, nucleR, oneChannelGUI, PING, PSICQUIC, rfPred, rGADEM, RIPSeeker, rMAT, Rsamtools, rSFFreader, segmentSeq, 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, SplicingGraphs, TEQC, TFBSTools, triform, triplex, VariantAnnotation, VariantTools, XVector
Imports Me	AllelicImbalance, annmap, AnnotationDbi, ArrayExpressHTS, BayesPeak, Biostrings, biovizBase, BiSeq, BitSeq, CAGEr, cgdv17, charm, chipenrich, chipenrich.data, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cleaver, cn.mops, CNVrd2, cobindR, copynumber, customProDB, DECIPHER, DiffBind, EDASeq, ensemblVEP, epigenomix, fastseg, flipflop, flowQ, FunciSNP, gCMAPWeb, GenomicFeatures, GenomicRanges, genoset, ggbio, girafe, gmapR, Gviz, h5vc, HTSeqGenie, HTSFilter, intansv, MEDIPS, methVisual, methyAnalysis, MethylSeekR, minfi, 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.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, PICS, plethy, prebs, QuasR, R453Plus1Toolbox, Rcade, REDseq, Repitools, ReportingTools, rGADEM, rMAT, rnaSeqMap, Rolexa, rSFFreader, RSVSim, rtracklayer, segmentSeq, SeqArray, SeqVarTools, 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, spliceR, SplicingGraphs, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantTools, waveTiling, XVector
Suggests Me	BiocGenerics, HilbertVis, HilbertVisGUI, MiRaGE, SNPchip, yeastRNASeq

Package Archives

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

Package Source	IRanges_1.20.7.tar.gz
Windows Binary	IRanges_1.20.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	IRanges_1.20.7.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats