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Bioconductor - GenomicRanges (development version)

GenomicRanges

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

Representation and manipulation of genomic intervals

Bioconductor version: Development (3.22)

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: Patrick Aboyoun [aut], HervÃ© PagÃ¨s [aut, cre], Michael Lawrence [aut], Sonali Arora [ctb], Martin Morgan [ctb], Kayla Morrell [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Lori Shepherd [ctb], Dan Tenenbaum [ctb], Daniel van Twisk [ctb]

Maintainer: HervÃ© PagÃ¨s <hpages.on.github at gmail.com>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

1. An Introduction to the GenomicRanges Package HTML 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 R Script Reference Manual PDF NEWS Text Details biocViews Annotation, Coverage, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software Version 1.61.1 In Bioconductor since BioC 2.6 (R-2.11) (15 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, stats4, BiocGenerics(>= 0.53.2), S4Vectors(>= 0.45.2), IRanges(>= 2.41.1), Seqinfo Imports utils, stats, XVector(>= 0.29.2) System Requirements URL https://bioconductor.org/packages/GenomicRanges Bug Reports https://github.com/Bioconductor/GenomicRanges/issues See More Suggests GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings(>= 2.77.2), SummarizedExperiment(>= 1.39.1), Rsamtools, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle Linking To S4Vectors, IRanges Enhances Depends On Me alabaster.ranges, AllelicImbalance, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, betaHMM, BindingSiteFinder, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, chimeraviz, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, CINdex, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, Cogito, consensusSeekeR, CSAR, csaw, CSSQ, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DNAshapeR, easylift, EnrichedHeatmap, ensembldb, epigenomix, esATAC, ExCluster, extraChIPs, fastseg, fCCAC, FindIT2, GeneBreak, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicPlot, GenomicScores, GenomicTuples, gmapR, gmoviz, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, HERON, hiAnnotator, HiCDOC, HiTC, IdeoViz, igvR, igvShiny, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, m6Aboost, maser, MBASED, Melissa, metagene2, methimpute, methodical, methylKit, methylPipe, minfi, MotifDb, motifTestR, msgbsR, MutationalPatterns, NADfinder, oncoscanR, ORFik, periodicDNA, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, recoup, regioneR, RepViz, rGREAT, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RNAmodR, RnBeads, Rsamtools, RSVSim, rtracklayer, SARC, Scale4C, SCOPE, segmentSeq, seqArchRplus, seqCAT, SeqGate, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SomaticSignatures, spiky, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, tadar, TnT, trackViewer, transmogR, traseR, tRNA, tRNAdbImport, tRNAscanImport, txdbmaker, VanillaICE, VarCon, VariantAnnotation, VariantTools, VplotR, vtpnet, vulcan, wavClusteR, YAPSA, EuPathDB, excluderanges, ChAMPdata, EatonEtAlChIPseq, nullrangesData, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, WGSmapp, liftOver, sequencing, PlasmaMutationDetector, rnaCrosslinkOO, RTIGER Imports Me ACE, alabaster.se, ALDEx2, amplican, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ASpli, AssessORF, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, ballgown, bambu, bamsignals, baySeq, BBCAnalyzer, beadarray, BEAT, bedbaser, BiFET, BioTIP, biovizBase, biscuiteer, BiSeq, BOBaFIT, borealis, branchpointer, BREW3R.r, BSgenomeForge, BUSpaRse, cageminer, CAGEr, cardelino, cBioPortalData, CexoR, cfdnakit, cfDNAPro, cfTools, chipenrich, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, chromVAR, cicero, circRNAprofiler, cleanUpdTSeq, CleanUpRNAseq, cliProfiler, CNVfilteR, CNViz, CNVMetrics, comapr, coMethDMR, conumee, CopyNumberPlots, CoverageView, crisprBase, crisprBowtie, crisprDesign, CRISPRseek, CrispRVariants, crisprViz, crupR, CTexploreR, customProDB, DAMEfinder, Damsel, debrowser, decompTumor2Sig, deconvR, DEFormats, DegCre, DegNorm, deltaCaptureC, derfinder, derfinderPlot, DEWSeq, diffUTR, dinoR, DMRcate, dmrseq, DNAfusion, DominoEffect, doubletrouble, DRIMSeq, DropletUtils, DuplexDiscovereR, easyRNASeq, EDASeq, EDIRquery, eisaR, ELMER, ELViS, enhancerHomologSearch, epialleleR, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epiregulon, epistack, EpiTxDb, epivizr, epivizrData, EventPointer, factR, fcScan, FilterFFPE, fishpond, FLAMES, FRASER, G4SNVHunter, GA4GHclient, gcapc, gDNAx, geneAttribution, GENESIS, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicInteractionNodes, GenomicInteractions, GenVisR, geomeTriD, ggbio, gINTomics, GOfuncR, GrafGen, GRaNIE, gwascat, h5vc, heatmaps, hermes, HicAggR, HiCBricks, HiCcompare, HiCExperiment, HiContacts, HiCool, HiCParser, hicVennDiagram, HilbertCurve, HiLDA, hiReadsProcessor, hummingbird, icetea, ideal, idr2d, IMAS, iNETgrate, INSPEcT, ipdDb, IsoformSwitchAnalyzeR, isomiRs, IVAS, karyoploteR, katdetectr, knowYourCG, loci2path, LOLA, LoomExperiment, lumi, magpie, mariner, mCSEA, MDTS, MEAL, MEDIPS, megadepth, memes, metaseqR2, methInheritSim, MethReg, methrix, methylCC, methylInheritance, MethylSeekR, methylSig, methylumi, MinimumDistance, MIRA, missMethyl, mitoClone2, MMDiff2, mobileRNA, Modstrings, monaLisa, Moonlight2R, mosaics, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, MouseFM, MSA2dist, MultiAssayExperiment, multicrispr, MultiDataSet, multiHiCcompare, MungeSumstats, musicatk, NanoMethViz, ncRNAtools, nearBynding, normr, nucleR, nullranges, OGRE, oligoClasses, OmaDB, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, pageRank, panelcn.mops, partCNV, PAST, pcaExplorer, pepStat, pgxRpi, PhIPData, PICB, PIPETS, plotgardener, plyinteractions, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, Pviz, QDNAseq, qpgraph, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, raer, RAIDS, ramr, RareVariantVis, RCAS, RcisTarget, recount, recount3, regionalpcs, regioneR, regionReport, regutools, REMP, Repitools, RESOLVE, rfPred, RgnTX, Rhisat2, RiboCrypt, RiboDiPA, RiboProfiling, rigvf, Rmmquant, rmspc, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, RTCGAToolbox, saseR, scanMiR, scanMiRApp, scDblFinder, scmeth, scoreInvHap, scPipe, scRNAseqApp, scruff, scuttle, segmenter, seq2pathway, SeqArray, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sevenC, shinyepico, ShortRead, signeR, SigsPack, SimFFPE, SingleCellExperiment, SingleMoleculeFootprinting, sitadela, Site2Target, snapcount, soGGi, SOMNiBUS, SparseSignatures, spatzie, SpectralTAD, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, syntenet, systemPipeR, TAPseq, target, TCGAbiolinks, TCGAutils, TCseq, TDbasedUFE, TDbasedUFEadv, TENET, TENxIO, terraTCGAdata, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, tidybulk, tidyCoverage, tLOH, tracktables, transcriptR, transite, TRESS, tricycle, triplex, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, Uniquorn, UPDhmm, VariantFiltering, VaSP, VCFArray, vmrseq, wiggleplotr, xcore, ZygosityPredictor, BioMartGOGeneSets, fitCons.UCSC.hg19, 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.v4.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, TENET.AnnotationHub, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, BioPlex, biscuiteerData, chipenrich.data, COSMIC.67, ELMER.data, fourDNData, GenomicDistributionsData, leeBamViews, mCSEAdata, MethylSeqData, pepDat, scMultiome, scRNAseq, sesameData, SomaticCancerAlterations, spatialLIBD, TENET.ExperimentHub, TumourMethData, VariantToolsData, ExpHunterSuite, recountWorkflow, seqpac, cinaR, cpp11bigwig, crispRdesignR, driveR, GencoDymo2, geneHapR, geno2proteo, GenoPop, hahmmr, HiCociety, hoardeR, ICAMS, karyotapR, locuszoomr, lolliplot, LoopRig, MAAPER, MitoHEAR, noisyr, numbat, oncoPredict, PACVr, RapidoPGS, revert, SATS, scPloidy, Signac, tepr, VALERIE Suggests Me AlphaMissenseR, AnnotationHub, autonomics, biobroom, BiocGenerics, BiocParallel, CCAFE, Chicago, ComplexHeatmap, cummeRbund, DFplyr, epivizrChart, GenomeInfoDb, ggmanh, Glimma, GSReg, GWASTools, HDF5Array, InteractiveComplexHeatmap, interactiveDisplay, IRanges, iSEE, lute, maftools, MiRaGE, MIRit, omicsPrint, parglms, recountmethylation, RTCGA, 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