IRanges

DOI: 10.18129/B9.bioc.IRanges    

Infrastructure for manipulating intervals on sequences

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	2.12.0
In Bioconductor since	BioC 2.3 (R-2.8) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.23.3), S4Vectors(>= 0.15.5)
Imports	stats4
LinkingTo	S4Vectors
Suggests	XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit
SystemRequirements
Enhances
URL
Depends On Me	AnnotationDbi, AnnotationHubData, BaalChIP, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, BubbleTree, bumphunter, CAFE, casper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, CNPBayes, CODEX, consensusSeekeR, CSAR, customProDB, deepSNV, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCHMM, DMRcaller, epigenomix, exomeCopy, fCCAC, FunciSNP.data, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, groHMM, gtrellis, Guitar, Gviz, harbChIP, HelloRanges, HilbertCurve, HiTC, HMMcopy, htSeqTools, IdeoViz, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, NADfinder, oneChannelGUI, 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, 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, AnnotationDbi, annotatr, ArrayExpressHTS, ASpli, ATACseqQC, ballgown, bamsignals, BasicSTARRseq, BayesPeak, BBCAnalyzer, beadarray, biovizBase, BiSeq, BitSeq, bnbc, BPRMeth, branchpointer, BSgenome, bsseq, BUMHMM, CAGEr, cgdv17, charm, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, chromstaR, chromswitch, chromVAR, CINdex, cleaver, cn.mops, CNEr, CNVPanelizer, CNVrd2, cobindR, coMET, compEpiTools, contiBAIT, conumee, copynumber, CopywriteR, CoverageView, CRISPRseek, CrispRVariants, csaw, customProDB, debrowser, DECIPHER, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DiffBind, diffHic, diffloop, DMRcate, DMRScan, DOQTL, DRIMSeq, easyRNASeq, EDASeq, ELMER, EnrichedHeatmap, ensembldb, epivizr, epivizrData, esATAC, facopy, fastseg, FindMyFriends, fitCons.UCSC.hg19, flipflop, flowQ, FunciSNP, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicFiles, GenomicInteractions, GenomicScores, GenomicTuples, genoset, genotypeeval, GenVisR, GGBase, ggbio, GGtools, girafe, gmapR, GoogleGenomics, GOpro, GOTHiC, gQTLstats, GUIDEseq, gwascat, h5vc, HDF5Array, heatmaps, HiCcompare, HTSeqGenie, ideal, IMAS, InPAS, INSPEcT, intansv, InteractionSet, IntEREst, InterMineR, IsoformSwitchAnalyzeR, isomiRs, IVAS, IWTomics, JunctionSeq, karyoploteR, LOLA, M3D, MADSEQ, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg38, MatrixRider, MEAL, MEDIPS, metagene, methimpute, methInheritSim, methVisual, methyAnalysis, methylInheritance, methylKit, methylPipe, MethylSeekR, methylumi, methyvim, minfi, MinimumDistance, MIRA, mosaics, motifbreakR, motifmatchr, motifRG, MotIV, msa, msgbsR, MSnbase, MultiAssayExperiment, MultiDataSet, MutationalPatterns, NarrowPeaks, normr, nucleoSim, nucleR, oligoClasses, openPrimeR, Organism.dplyr, OrganismDbi, 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, PureCN, Pviz, QDNAseq, qpgraph, 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, SeqSQC, SeqVarTools, ShortRead, simulatorZ, skewr, 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, soGGi, SomaticCancerAlterations, SomaticSignatures, spliceR, spliceSites, SplicingGraphs, SPLINTER, STAN, SummarizedExperiment, SVM2CRM, TarSeqQC, TCGAbiolinks, TCseq, TFBSTools, TFHAZ, TitanCNA, TnT, tracktables, trackViewer, transcriptR, TransView, triform, TSRchitect, TSSi, TVTB, 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, gQTLBase, GWASTools, HilbertVis, HilbertVisGUI, MiRaGE, regionReport, RTCGA, S4Vectors, yeastRNASeq
Build Report

Package Archives

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

Source Package	IRanges_2.12.0.tar.gz
Windows Binary	IRanges_2.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	IRanges_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IRanges
Package Short Url	http://bioconductor.org/packages/IRanges/
Package Downloads Report	Download Stats