GenomicRanges

DOI: 10.18129/B9.bioc.GenomicRanges    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges.

Representation and manipulation of genomic intervals

Bioconductor version: 3.10

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicRanges")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("GenomicRanges")

 

HTML	R Script	1. An Introduction to the GenomicRanges Package
PDF	R Script	2. GenomicRanges HOWTOs
PDF	R Script	3. A quick introduction to GRanges and GRangesList objects (slides)
PDF	R Script	4. Ten Things You Didn't Know (slides from BioC 2016)
PDF	R Script	5. Extending GenomicRanges
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 2.6 (R-2.11) (10 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, stats4, BiocGenerics(>= 0.25.3), S4Vectors(>= 0.23.19), IRanges(>= 2.19.9), GenomeInfoDb(>= 1.15.2)
Imports	utils, stats, XVector(>= 0.19.8)
LinkingTo	S4Vectors, IRanges
Suggests	Matrix, Biobase, AnnotationDbi, annotate, Biostrings(>= 2.25.3), SummarizedExperiment(>= 0.1.5), Rsamtools(>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, baySeq, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, CHARGE, chimera, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chroGPS, chromPlot, chromstaR, chromswitch, CINdex, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, compEpiTools, consensusSeekeR, CSAR, csaw, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DMRforPairs, DNAshapeR, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, epihet, esATAC, EuPathDB, ExCluster, exomeCopy, fastseg, fCCAC, FourCSeq, FunChIP, GeneBreak, geneRxCluster, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicScores, GenomicTuples, genoset, geuvStore2, gmapR, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, hiAnnotator, HiTC, IdeoViz, igvR, InPAS, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, maser, MBASED, Melissa, metagene, metagene2, methimpute, methyAnalysis, methylKit, methylPipe, minfi, MotIV, msgbsR, MutationalPatterns, NADfinder, OmicCircos, ORFik, PGA, PING, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, Rariant, Rcade, recoup, regioneR, RepViz, rfPred, rGREAT, riboSeqR, RIPSeeker, RJMCMCNucleosomes, RNAmodR, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, segmentSeq, seqbias, seqCAT, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomaticSignatures, StructuralVariantAnnotation, SummarizedExperiment, TarSeqQC, TnT, trackViewer, TransView, traseR, tRNA, tRNAdbImport, tRNAscanImport, VanillaICE, VariantAnnotation, VariantExperiment, VariantTools, vtpnet, vulcan, wavClusteR, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, YAPSA
Imports Me	ACE, ALDEx2, alpine, ALPS, amplican, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, AssessORF, ATACseqQC, BadRegionFinder, ballgown, bamsignals, BBCAnalyzer, beadarray, BEAT, BiFET, BiocOncoTK, BioTIP, biovizBase, biscuiteer, BiSeq, brainflowprobes, branchpointer, BSgenome, BUSpaRse, CAGEr, CexoR, cgdv17, ChAMP, ChIC, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, ChIPSeqSpike, chromDraw, ChromHeatMap, chromVAR, cicero, circRNAprofiler, cleanUpdTSeq, CNEr, CNVfilteR, coMET, compartmap, contiBAIT, conumee, copynumber, CopyNumberPlots, CopywriteR, COSMIC.67, CoverageView, crisprseekplus, CrispRVariants, customProDB, DChIPRep, debrowser, decompTumor2Sig, DeepBlueR, DEFormats, deltaCaptureC, derfinder, derfinderPlot, DEWSeq, diffloop, DMRcate, DMRScan, dmrseq, DominoEffect, DRIMSeq, easyRNASeq, EDASeq, ELMER, ELMER.data, ENCODExplorer, enrichTF, epivizr, epivizrData, erma, EventPointer, fcScan, fitCons.UCSC.hg19, flipflop, FourCSeq, FunciSNP, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicInteractions, genotypeeval, GenVisR, GGBase, ggbio, GGtools, GOfuncR, gpart, gQTLBase, gQTLstats, gwascat, h5vc, heatmaps, HiCBricks, HiCcompare, HilbertCurve, HiLDA, hiReadsProcessor, HTSeqGenie, icetea, ideal, idr2d, IMAS, INSPEcT, InterMineR, ipdDb, IsoformSwitchAnalyzeR, isomiRs, iteremoval, IVAS, JunctionSeq, karyoploteR, leeBamViews, loci2path, LOLA, LoomExperiment, lumi, M3D, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomAD.r3.0.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, mCSEA, MDTS, MEAL, MEDIPS, MetaNeighbor, MethCP, methInheritSim, methyAnalysis, methylCC, methylInheritance, MethylSeekR, methylumi, MinimumDistance, MIRA, MMAPPR2, MMDiff2, Modstrings, mosaics, motifbreakR, motifmatchr, MTseeker, MTseekerData, MultiAssayExperiment, MultiDataSet, multiHiCcompare, NarrowPeaks, normr, nucleR, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, panelcn.mops, PAST, Pbase, pcaExplorer, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, PICS, pqsfinder, pram, prebs, PrecisionTrialDrawer, primirTSS, proBAMr, profileplyr, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, qPLEXanalyzer, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, RareVariantVis, RCAS, rCGH, recount, recountWorkflow, regioneR, regionReport, REMP, Repitools, rGADEM, RGMQL, Rhisat2, RiboProfiling, Rmmquant, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAprobR, rnaSeqMap, roar, RTCGAToolbox, scmeth, scoreInvHap, scPipe, scruff, seq2pathway, SeqArray, seqPattern, seqplots, seqsetvis, SeqSQC, SeqVarTools, sesame, sevenC, ShortRead, signeR, SigsPack, simulatorZ, SNPchip, 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, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticCancerAlterations, SparseSignatures, SpectralTAD, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, systemPipeR, target, TCGAbiolinks, TCGAutils, TCGAWorkflow, TCseq, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, TitanCNA, tracktables, transcriptR, transite, trena, triplex, TSRchitect, TVTB, tximeta, TxRegInfra, Ularcirc, Uniquorn, VariantFiltering, VariantToolsData, VCFArray, waveTiling, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, yriMulti
Suggests Me	alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, CAGEWorkflow, Chicago, ComplexHeatmap, cummeRbund, epivizrChart, GenomeInfoDb, GenomicState, GeuvadisTranscriptExpr, Glimma, GSReg, GWASTools, HDF5Array, interactiveDisplay, IRanges, metaseqR, methrix, MiRaGE, nanotubes, NarrowPeaks, omicsPrint, Onassis, parglms, RNAmodR.Data, RTCGA, S4Vectors, SeqGSEA, sesameData, Single.mTEC.Transcriptomes, TFutils
Links To Me
Build Report

Package Archives

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

Source Package	GenomicRanges_1.38.0.tar.gz
Windows Binary	GenomicRanges_1.38.0.zip
Mac OS X 10.11 (El Capitan)	GenomicRanges_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicRanges
Source Repository (Developer Access)	git clone [email protected]:packages/GenomicRanges
Package Short Url	https://bioconductor.org/packages/GenomicRanges/
Package Downloads Report	Download Stats