To install this package, start R and enter:

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

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

GenomicRanges

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals and variables defined along a genome

Bioconductor version: 3.2

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure.

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

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicRanges")):

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("GenomicRanges")

PDF		A quick introduction to GRanges and GRangesList objects
PDF		An Introduction to GenomicRanges
PDF		Extending GenomicRanges
PDF		GenomicRanges HOWTOs
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.22.4
In Bioconductor since	BioC 2.6 (R-2.11) (6 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.16.1), S4Vectors(>= 0.8.6), IRanges(>= 2.4.6), GenomeInfoDb(>= 1.1.20)
Imports	utils, stats, XVector
LinkingTo	S4Vectors, IRanges
Suggests	Biobase, AnnotationDbi(>= 1.21.1), annotate, Biostrings(>= 2.25.3), Rsamtools(>= 1.13.53), SummarizedExperiment(>= 0.1.5), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
Depends On Me	AllelicImbalance, annmap, AnnotationHubData, Basic4Cseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, casper, cheung2010, chimera, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, cleanUpdTSeq, cn.mops, CNPBayes, cnvGSA, CNVPanelizer, compEpiTools, CSAR, csaw, DASiR, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DMRcaller, DMRcatedata, DMRforPairs, DOQTL, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, exomeCopy, fastseg, FourCSeq, GeneBreak, geneRxCluster, genomes, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicTuples, genoset, GenoView, geuvStore, ggtut, gmapR, GOTHiC, GreyListChIP, groHMM, Guitar, Gviz, hiAnnotator, HilbertCurve, HiTC, htSeqTools, IdeoViz, InPAS, intansv, MBASED, metagene, methyAnalysis, methylPipe, minfi, MMDiff, OmicCircos, PGA, PING, podkat, QuasR, r3Cseq, Rariant, Rcade, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, segmentSeq, seqbias, SGSeq, SigFuge, 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, SomatiCA, SomaticSignatures, SummarizedExperiment, TarSeqQC, trackViewer, TransView, traseR, VanillaICE, VariantAnnotation, VariantTools, vtpnet, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me	ALDEx2, ArrayExpressHTS, ballgown, bamsignals, beadarray, BEAT, biovizBase, BiSeq, BSgenome, CAGEr, CexoR, cgdv17, ChAMP, chipenrich, chipenrich.data, ChIPseeker, chipseq, ChIPseqR, chromDraw, CNEr, coMET, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, customProDB, DChIPRep, derfinder, derfinderPlot, DMRcate, easyRNASeq, EDASeq, ELMER, ELMER.data, epivizr, erma, flipflop, FourCSeq, FunciSNP, genomation, genomeIntervals, GenomicAlignments, GenomicInteractions, genotypeeval, GGBase, ggbio, GGtools, GoogleGenomics, gQTLBase, gQTLstats, GUIDEseq, gwascat, h5vc, hiReadsProcessor, HTSeqGenie, INSPEcT, IVAS, LedPred, leeBamViews, LOLA, lumi, 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, MEAL, MEDIPS, methyAnalysis, MethylSeekR, methylumi, MinimumDistance, MMDiff, motifbreakR, NarrowPeaks, nucleR, oligoClasses, OrganismDbi, Pbase, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PICS, prebs, proBAMr, Pviz, pwOmics, qpgraph, R3CPET, R453Plus1Toolbox, RareVariantVis, rCGH, regioneR, regionReport, Repitools, rgsepd, RiboProfiling, RNAprobR, rnaSeqMap, roar, seq2pathway, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, SICtools, simulatorZ, SNPchip, 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, spliceR, SplicingGraphs, SVM2CRM, systemPipeR, TCGAbiolinks, TFBSTools, ToPASeq, tracktables, triplex, VariantFiltering, waveTiling, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me	AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, cummeRbund, GenomeInfoDb, gtrellis, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, SeqGSEA, STAN
Build Report

Package Archives

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

Package Source	GenomicRanges_1.22.4.tar.gz
Windows Binary	GenomicRanges_1.22.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicRanges_1.22.1.tgz
Mac OS X 10.9 (Mavericks)	GenomicRanges_1.22.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/GenomicRanges/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/GenomicRanges/
Package Downloads Report	Download Stats

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