To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IRanges")

In most cases, you don't need to download the package archive at all.

IRanges

 

   

This is the development version of IRanges; for the stable release version, see IRanges.

Infrastructure for manipulating intervals on sequences

Bioconductor version: Development (3.4)

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. Pag├Ęs, 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 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

Details

biocViews DataRepresentation, Infrastructure, Software
Version 2.7.12
In Bioconductor since BioC 2.3 (R-2.8) (8 years)
License Artistic-2.0
Depends R (>= 3.1.0), methods, utils, stats, BiocGenerics(>= 0.19.1), S4Vectors(>= 0.11.2)
Imports stats4
LinkingTo S4Vectors
Suggests XVector, GenomicRanges, GenomicFeatures, GenomicAlignments, BSgenome.Celegans.UCSC.ce2, RUnit
SystemRequirements
Enhances
URL
Depends On Me AnnotationDbi, AnnotationHubData, ASpli, BayesPeak, biomvRCNS, Biostrings, BiSeq, BSgenome, BubbleTree, bumphunter, CAFE, casper, CexoR, ChIPComp, ChIPpeakAnno, chipseq, chroGPS, CODEX, consensusSeekeR, CSAR, customProDB, deepSNV, DESeq2, DEXSeq, DirichletMultinomial, DMRcaller, EnrichedHeatmap, epigenomix, exomeCopy, FunciSNP.data, geneRxCluster, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, Genominator, groHMM, gtrellis, Guitar, Gviz, harbChIP, HDF5Array, HilbertCurve, HiTC, HMMcopy, htSeqTools, IdeoViz, isomiRs, LiebermanAidenHiC2009, methyAnalysis, MotifDb, motifRG, oneChannelGUI, OTUbase, pepStat, PGA, PING, proBAMr, PSICQUIC, RefNet, rfPred, rGADEM, rGREAT, RIPSeeker, scsR, segmentSeq, SGSeq, SICtools, SomatiCA, TEQC, TitanCNA, traseR, triform, triplex, VariantTools, XVector
Imports Me ALDEx2, AllelicImbalance, AneuFinder, annmap, AnnotationDbi, ArrayExpressHTS, ballgown, bamsignals, BasicSTARRseq, BayesPeak, BBCAnalyzer, beadarray, Biostrings, biovizBase, BiSeq, BitSeq, BSgenome, bsseq, CAGEr, cgdv17, charm, chipenrich, chipenrich.data, ChIPQC, ChIPseeker, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, chromstaR, CINdex, cleaver, clusterProfiler, cn.mops, CNEr, CNPBayes, CNVPanelizer, CNVrd2, cobindR, coMET, compEpiTools, contiBAIT, conumee, copynumber, CopywriteR, CoverageView, CRISPRseek, CrispRVariants, csaw, customProDB, debrowser, DECIPHER, derfinder, derfinderHelper, derfinderPlot, DiffBind, diffHic, diffloop, DMRcate, DOQTL, DRIMSeq, easyRNASeq, EDASeq, ensembldb, epivizr, epivizrData, facopy, fastseg, FindMyFriends, flipflop, flowQ, FunciSNP, genbankr, GeneGeneInteR, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicFiles, GenomicInteractions, GenomicTuples, genoset, genotypeeval, GenVisR, GGBase, ggbio, GGtools, girafe, gmapR, GoogleGenomics, GOTHiC, gQTLstats, GUIDEseq, gwascat, h5vc, HTSeqGenie, InPAS, INSPEcT, intansv, InteractionSet, IVAS, JunctionSeq, LOLA, M3D, MADSEQ, MatrixRider, MEAL, MEDIPS, metagene, methVisual, methyAnalysis, methylKit, methylPipe, MethylSeekR, methylumi, minfi, MinimumDistance, mosaics, motifbreakR, motifRG, MotIV, msa, MSnbase, MultiAssayExperiment, MultiDataSet, NarrowPeaks, normr, nucleoSim, nucleR, oligoClasses, OrganismDbi, Pbase, pcaExplorer, pd.atdschip.tiling, pdInfoBuilder, PICS, PING, plethy, podkat, polyester, pqsfinder, prebs, PureCN, Pviz, QDNAseq, qpgraph, qsea, QuasR, R3CPET, r3Cseq, R453Plus1Toolbox, RareVariantVis, Rariant, Rcade, rCGH, REDseq, regioneR, ReportingTools, rGADEM, RiboProfiling, rnaSeqMap, RnBeads, roar, Rqc, Rsamtools, rSFFreader, RSVSim, RTN, rtracklayer, SCAN.UPC, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, simulatorZ, skewr, SMITE, SNPchip, SNPhood, soGGi, SomatiCA, SomaticCancerAlterations, SomaticSignatures, spliceR, spliceSites, SplicingGraphs, STAN, SummarizedExperiment, SVM2CRM, TarSeqQC, TCGAbiolinks, TFBSTools, tracktables, trackViewer, transcriptR, TransView, triform, TSSi, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, waveTiling, XVector
Suggests Me AnnotationHub, BaseSpaceR, BiocGenerics, Chicago, ClassifyR, gQTLBase, HilbertVis, HilbertVisGUI, MiRaGE, regionReport, RTCGA, S4Vectors, yeastRNASeq
Build Report  

Package Archives

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

Package Source IRanges_2.7.12.tar.gz
Windows Binary IRanges_2.7.12.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) IRanges_2.7.12.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/IRanges
Package Short Url http://bioconductor.org/packages/IRanges/
Package Downloads Report Download Stats

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