GenomicRanges

DOI: 10.18129/B9.bioc.GenomicRanges    

Representation and manipulation of genomic intervals

Bioconductor version: Release (3.15)

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 (version "4.2") and enter:

if (!require("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, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.48.0
In Bioconductor since BioC 2.6 (R-2.11) (12.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, stats4, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.15.2)
Imports utils, stats, XVector(>= 0.29.2)
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, KEGGREST, 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, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL https://bioconductor.org/packages/GenomicRanges
BugReports https://github.com/Bioconductor/GenomicRanges/issues
Depends On Me AllelicImbalance, AneuFinder, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, baySeq, BindingSiteFinder, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, chromstaR, chromswitch, CINdex, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, Cogito, compEpiTools, consensusSeekeR, CSAR, csaw, CSSQ, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DMRforPairs, DNAshapeR, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, ensemblVEP, epigenomix, epihet, esATAC, EuPathDB, ExCluster, exomeCopy, extraChIPs, fastseg, fCCAC, FindIT2, FunChIP, GeneBreak, geneRxCluster, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicScores, GenomicTuples, gmapR, gmoviz, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, hiAnnotator, HiTC, IdeoViz, igvR, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, m6Aboost, maser, MBASED, Melissa, metagene, metagene2, methimpute, methylKit, methylPipe, minfi, MotifDb, msgbsR, MutationalPatterns, NADfinder, nullrangesData, OmicCircos, ORFik, periodicDNA, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, ramr, Rcade, recoup, regioneR, RepViz, rGREAT, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RNAmodR, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, SCATEData, SCOPE, segmentSeq, seqbias, seqCAT, SeqGate, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SomaticSignatures, spiky, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, TarSeqQC, TnT, trackViewer, TransView, traseR, tRNA, tRNAdbImport, tRNAscanImport, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantTools, VplotR, vtpnet, vulcan, wavClusteR, WGSmapp, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, YAPSA
Imports Me ACE, ALDEx2, alpine, amplican, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ArrayExpressHTS, ASpediaFI, ASpli, AssessORF, ATACseqQC, atena, BadRegionFinder, ballgown, bambu, bamsignals, BBCAnalyzer, beadarray, BEAT, BiFET, BiocOncoTK, BioPlex, BioTIP, biovizBase, biscuiteer, BiSeq, BOBaFIT, borealis, brainflowprobes, branchpointer, BRGenomics, BSgenome, BUSpaRse, cageminer, CAGEr, cBioPortalData, CexoR, ChAMP, ChIC, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, ChromSCape, chromVAR, cicero, circRNAprofiler, cleanUpdTSeq, cliProfiler, CNEr, CNVfilteR, CNViz, CNVMetrics, comapr, coMET, coMethDMR, compartmap, contiBAIT, conumee, copynumber, CopyNumberPlots, CopywriteR, COSMIC.67, CoverageView, crisprBase, crisprBowtie, CRISPRseek, crisprseekplus, CrispRVariants, customProDB, DAMEfinder, dasper, debrowser, decompTumor2Sig, deconvR, DeepBlueR, DEFormats, DegNorm, deltaCaptureC, derfinder, derfinderPlot, DEWSeq, diffloop, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, DRIMSeq, DropletUtils, easyRNASeq, EDASeq, eisaR, ELMER, ELMER.data, enhancerHomologSearch, enrichTF, epialleleR, EpiCompare, epidecodeR, epigraHMM, epimutacions, epistack, EpiTxDb, epivizr, epivizrData, erma, EventPointer, exomePeak2, fcScan, FilterFFPE, fishpond, fitCons.UCSC.hg19, FLAMES, FRASER, GA4GHclient, gcapc, genbankr, geneAttribution, GeneGeneInteR, GENESIS, GeneStructureTools, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicDistributionsData, GenomicInteractionNodes, GenomicInteractions, genotypeeval, GenVisR, ggbio, GOfuncR, gpart, GRaNIE, gwascat, h5vc, heatmaps, hermes, HiCBricks, HiCcompare, HiCDCPlus, HilbertCurve, HiLDA, hiReadsProcessor, HTSeqGenie, hummingbird, icetea, ideal, idr2d, IMAS, InPAS, INSPEcT, InterMineR, ipdDb, IsoformSwitchAnalyzeR, isomiRs, iteremoval, IVAS, karyoploteR, leeBamViews, loci2path, LOLA, LoomExperiment, lumi, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.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.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, mCSEA, MDTS, MEAL, MEDIPS, megadepth, memes, metaseqR2, MethCP, methInheritSim, MethReg, methrix, methylCC, methylInheritance, MethylSeekR, MethylSeqData, methylSig, methylumi, MinimumDistance, MIRA, missMethyl, mitoClone2, MMAPPR2, MMDiff2, Modstrings, monaLisa, mosaics, Motif2Site, motifbreakR, motifmatchr, MouseFM, MSA2dist, MultiAssayExperiment, multicrispr, MultiDataSet, multiHiCcompare, MungeSumstats, musicatk, NanoMethViz, nanotatoR, ncRNAtools, nearBynding, netDx, NoRCE, normr, nucleR, nullranges, NxtIRFcore, ODER, OGRE, oligoClasses, OmaDB, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, packFinder, pageRank, panelcn.mops, PAST, pcaExplorer, pepDat, pepStat, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PhIPData, Pi, PICS, PING, pqsfinder, pram, prebs, preciseTAD, PrecisionTrialDrawer, primirTSS, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, Pviz, pwOmics, QDNAseq, qpgraph, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, RareVariantVis, RCAS, rCGH, RcisTarget, recount, recount3, recountWorkflow, regioneR, regionReport, regutools, REMP, Repitools, rfPred, rGADEM, RGMQL, Rhisat2, RiboCrypt, RiboDiPA, RiboProfiling, RIPAT, RLSeq, Rmmquant, rmspc, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, RTCGAToolbox, scanMiR, scanMiRApp, SCATE, scDblFinder, scmeth, scoreInvHap, scPipe, scRNAseq, scruff, scuttle, segmenter, seq2pathway, SeqArray, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, shinyepico, ShortRead, signeR, SigsPack, SimFFPE, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, snapcount, 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, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SparseSignatures, spatialLIBD, spatzie, SpectralTAD, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, systemPipeR, TAPseq, target, TCGAbiolinks, TCGAutils, TCGAWorkflow, TCseq, terraTCGAdata, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, tidybulk, TitanCNA, tLOH, tracktables, transcriptR, transite, trena, TRESS, tricycle, triplex, tscR, TSRchitect, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, Uniquorn, VariantFiltering, VariantToolsData, VaSP, VCFArray, wiggleplotr, xcore, XNAString, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, autonomics, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, CAGEWorkflow, Chicago, CNVgears, ComplexHeatmap, cummeRbund, epivizrChart, GenomeInfoDb, GenomicState, GeuvadisTranscriptExpr, ggmanh, Glimma, GSReg, GWASTools, HDF5Array, InteractiveComplexHeatmap, interactiveDisplay, IRanges, maftools, MiRaGE, nanotubes, omicsPrint, Onassis, parglms, plotgardener, recountmethylation, RNAmodR.Data, RTCGA, S4Vectors, SeqGSEA, Single.mTEC.Transcriptomes, splatter, systemPipeRdata, TFutils, universalmotif, updateObject, xcoredata
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Follow Installation instructions to use this package in your R session.

Source Package GenomicRanges_1.48.0.tar.gz
Windows Binary GenomicRanges_1.48.0.zip
macOS Binary (x86_64) GenomicRanges_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicRanges
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicRanges
Package Short Url https://bioconductor.org/packages/GenomicRanges/
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