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

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

Bioconductor version: Development (3.4)

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. Pag├Ęs, 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 R Script 10 Things You Didn't Know (slides from BioC 2016)
PDF R Script A quick introduction to GRanges and GRangesList objects (slides)
PDF R Script An Introduction to the GenomicRanges Package
PDF R Script Extending GenomicRanges
PDF R Script GenomicRanges HOWTOs
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.25.9
In Bioconductor since BioC 2.6 (R-2.11) (6 years)
License Artistic-2.0
Depends R (>= 2.10), methods, stats4, BiocGenerics(>= 0.17.5), S4Vectors(>= 0.9.47), IRanges(>= 2.7.8), 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), Matrix, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, 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, hgu95av2probe
SystemRequirements
Enhances
URL
Depends On Me AllelicImbalance, AneuFinder, annmap, AnnotationHubData, Basic4Cseq, BasicSTARRseq, baySeq, biomvRCNS, BiSeq, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, casper, ChAMPdata, cheung2010, chimera, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, CINdex, cleanUpdTSeq, cn.mops, CNPBayes, cnvGSA, CNVPanelizer, compEpiTools, consensusSeekeR, CSAR, csaw, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DMRcaller, DMRcatedata, DMRforPairs, DNAshapeR, DOQTL, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, exomeCopy, fastseg, FourCSeq, FunChIP, GeneBreak, geneRxCluster, GenoGAM, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicTuples, genoset, geuvStore2, gmapR, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, hiAnnotator, HilbertCurve, HiTC, htSeqTools, IdeoViz, InPAS, intansv, InteractionSet, isomiRs, MBASED, metagene, methyAnalysis, methylPipe, minfi, OmicCircos, PGA, PING, podkat, QuasR, r3Cseq, Rariant, Rcade, recoup, regioneR, rfPred, rGREAT, riboSeqR, RIPSeeker, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, segmentSeq, seqbias, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SomatiCA, SomaticSignatures, SummarizedExperiment, TarSeqQC, TitanCNA, trackViewer, TransView, traseR, VanillaICE, VariantAnnotation, VariantTools, vtpnet, wavClusteR, yriMulti
Imports Me ALDEx2, ArrayExpressHTS, BadRegionFinder, ballgown, bamsignals, BBCAnalyzer, beadarray, BEAT, biovizBase, BiSeq, BSgenome, CAGEr, CexoR, cgdv17, ChAMP, chipenrich, chipenrich.data, ChIPseeker, chipseq, ChIPseqR, chromDraw, CNEr, CNPBayes, coMET, contiBAIT, conumee, copynumber, CopywriteR, COSMIC.67, CoverageView, CrispRVariants, customProDB, DChIPRep, debrowser, DEFormats, derfinder, derfinderPlot, diffloop, DMRcate, DRIMSeq, easyRNASeq, EDASeq, ELMER.data, epivizr, epivizrData, erma, flipflop, FourCSeq, FunciSNP, genbankr, genomation, genomeIntervals, GenomicAlignments, GenomicInteractions, genotypeeval, GenVisR, GGBase, ggbio, GGtools, GoogleGenomics, gQTLBase, gQTLstats, gwascat, h5vc, hiReadsProcessor, HTSeqGenie, INSPEcT, IVAS, JunctionSeq, leeBamViews, LOLA, lumi, M3D, MADSEQ, MEAL, MEDIPS, methyAnalysis, MethylSeekR, methylumi, MinimumDistance, MMDiff2, mosaics, motifbreakR, MultiAssayExperiment, MultiDataSet, NarrowPeaks, nucleR, oligoClasses, OrganismDbi, Pbase, pcaExplorer, pepDat, pepStat, PICS, pqsfinder, prebs, proBAMr, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, R3CPET, R453Plus1Toolbox, RareVariantVis, rCGH, regioneR, regionReport, RiboProfiling, RNAprobR, rnaSeqMap, roar, seq2pathway, SeqArray, seqPattern, seqplots, SeqVarTools, ShortRead, simulatorZ, SNPchip, soGGi, SomatiCA, SomaticCancerAlterations, spliceR, SplicingGraphs, STAN, SVM2CRM, systemPipeR, TCGAbiolinks, TFBSTools, tracktables, transcriptR, triplex, VariantFiltering, waveTiling
Suggests Me AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, Chicago, cummeRbund, GenomeInfoDb, GeuvadisTranscriptExpr, HDF5Array, interactiveDisplay, IRanges, metaseqR, MiRaGE, NarrowPeaks, NGScopy, RTCGA, S4Vectors, SeqGSEA, Single.mTEC.Transcriptomes
Build Report  

Package Archives

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

Package Source GenomicRanges_1.25.9.tar.gz
Windows Binary GenomicRanges_1.25.1.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) GenomicRanges_1.25.9.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicRanges
Package Short Url http://bioconductor.org/packages/GenomicRanges/
Package Downloads Report Download Stats

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