GenomicRanges
Representation and manipulation of genomic intervals
Bioconductor version: 3.23 · Package version: 1.64.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicRanges")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| Author | Patrick Aboyoun [aut], Hervé Pagès [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] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/GenomicRanges |
| Bug Reports | https://github.com/Bioconductor/GenomicRanges/issues |
| Downloads rank | 53952 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, Coverage, DataRepresentation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
Documentation
- An Introduction to the GenomicRanges Package
- GenomicRanges HOWTOs
- A quick introduction to GRanges and GRangesList objects (slides)
- Ten Things You Didn't Know (slides from BioC 2016)
- Extending GenomicRanges
Download
Dependencies
Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.43.6), Seqinfo (>= 0.99.3)
Suggests: GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, UCSC.utils, 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.plantsmart51, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle
Reverse dependencies
Depends On Me (182): alabaster.ranges, AllelicImbalance, annmap, AnnotationHubData, BaalChIP, Basic4Cseq, BasicSTARRseq, betaHMM, BindingSiteFinder, biomvRCNS, BiSeq, bnbc, BPRMeth, breakpointR, BSgenome, bsseq, BubbleTree, bumphunter, CAFE, CAGEfightR, casper, ChAMPdata, chimeraviz, ChIPanalyser, ChIPComp, ChIPpeakAnno, ChIPQC, chipseq, chromPlot, cn.mops, cnvGSA, CNVPanelizer, CNVRanger, COCOA, Cogito, compEpiTools, consensusSeekeR, CSAR, csaw, CSSQ, deepSNV, DEScan2, DESeq2, DEXSeq, DiffBind, diffHic, DMCFB, DMCHMM, DMRcaller, DNAshapeR, easylift, EatonEtAlChIPseq, EnrichedHeatmap, ensembldb, epigenomix, esATAC, EuPathDB, excluderanges, ExCluster, extraChIPs, fastseg, fCCAC, FindIT2, fourSynergy, GeneBreak, geneRxCluster, GenomicAlignments, GenomicCoordinates, GenomicDistributions, GenomicFeatures, GenomicFiles, GenomicOZone, GenomicPlot, GenomicScores, GenomicTuples, gmapR, gmoviz, GMRP, GOTHiC, GreyListChIP, groHMM, gtrellis, GUIDEseq, Guitar, Gviz, HelloRanges, HERON, HiCDOC, HiTC, IdeoViz, igvR, igvShiny, InTAD, intansv, InteractionSet, IntEREst, IWTomics, karyoploteR, liftOver, linkSet, m6Aboost, maser, MBASED, Melissa, metagene2, methimpute, methodical, methylKit, methylPipe, minfi, MotifDb, motifTestR, msgbsR, MutationalPatterns, NADfinder, nullrangesData, OmicCircos, oncoscanR, ORFik, periodicDNA, PlasmaMutationDetector, plyranges, podkat, QuasR, r3Cseq, RaggedExperiment, recoup, regioneR, RepViz, rGREAT, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, rnaCrosslinkOO, RNAmodR, RnBeads, RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, Rsamtools, RSVSim, rtracklayer, Scale4C, SCOPE, segmentSeq, seqCAT, SeqGate, sequencing, SGSeq, SICtools, SigFuge, SMITE, SNPhood, SomaticSignatures, spiky, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, tadar, TnT, trackViewer, transmogR, traseR, tRNA, tRNAdbImport, tRNAscanImport, txdbmaker, UCSCRepeatMasker, VanillaICE, VarCon, VariantAnnotation, VariantExperiment, VariantTools, VplotR, vtpnet, vulcan, wavClusteR, WGSmapp, YAPSA
Imports Me (482): ACE, ActiveDriverWGS, alabaster.se, ALDEx2, amplican, annoLinker, AnnotationFilter, annotatr, APAlyzer, apeglm, appreci8R, ASpli, AssessORF, atacInferCnv, ATACseqQC, ATACseqTFEA, atena, BadRegionFinder, ballgown, bambu, bamsignals, baySeq, BBCAnalyzer, beadarray, BEAT, bedbaser, betterChromVAR, BiFET, Bioc.gff, BioMartGOGeneSets, BioTIP, biovizBase, biscuiteer, biscuiteerData, BiSeq, BOBaFIT, borealis, branchpointer, BREW3R.r, BSgenomeForge, BUSpaRse, cageminer, CAGEr, cardelino, cBioPortalData, CexoR, cfdnakit, cfDNAPro, cfTools, ChAMP, chipenrich, chipenrich.data, ChIPexoQual, ChIPseeker, chipseq, ChIPseqR, chromDraw, ChromHeatMap, ChromSCape, chromVAR, cicero, cinaR, circRNAprofiler, cleanUpdTSeq, CleanUpRNAseq, cliProfiler, ClonalSim, CNEr, CNVfilteR, CNViz, CNVMetrics, comapr, coMethDMR, conumee, CopyNumberPlots, COSMIC.67, CoverageView, cpp11bigwig, crisprBase, crisprBowtie, crisprDesign, crispRdesignR, CRISPRseek, CrispRVariants, crisprViz, crupR, CTexploreR, customProDB, DAMEfinder, damidBind, Damsel, debrowser, decemedip, decompTumor2Sig, deconvR, DEFormats, DegCre, DegNorm, deltaCaptureC, derfinder, derfinderPlot, DESNP, DEWSeq, diffUTR, dinoR, DMRcaller, DMRcate, DMRScan, dmrseq, DNAfusion, DominoEffect, DOTSeq, doubletrouble, DRIMSeq, driveR, DropletUtils, DuplexDiscovereR, easyRNASeq, EDASeq, EDIRquery, eisaR, ELMER, ELMER.data, ELViS, enhancerHomologSearch, epialleleR, EpiCompare, epidecodeR, epigraHMM, EpiMix, epimutacions, epiregulon, epiRomics, epiSeeker, epistack, EpiTxDb, epivizr, epivizrData, EventPointer, ExpHunterSuite, factR, fastRanges, fcScan, FilterFFPE, fishpond, fitCons.UCSC.hg19, FLAMES, fourDNData, fRagmentomics, FRASER, G4SNVHunter, GA4GHclient, gcapc, gDNAx, GencoDymo2, geneAttribution, GENESIS, GeneStructureTools, geno2proteo, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicDataCommons, GenomicDistributionsData, GenomicInteractionNodes, GenomicInteractions, GenoPop, GenVisR, geomeTriD, ggbio, gINTomics, GOaGO, GOfuncR, GrafGen, GRaNIE, gVenn, gwascat, h5vc, hahmmr, heatmaps, hermes, HicAggR, HiCaptuRe, HiCBricks, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, HiCParser, HiCPotts, hicream, hicVennDiagram, HilbertCurve, HiLDA, hummingbird, icetea, ideal, idr2d, IMAS, iNETgrate, InPAS, INSPEcT, ipdDb, IsoformSwitchAnalyzeR, isomiRs, IVAS, karyoploteR, karyotapR, katdetectr, knowYourCG, leeBamViews, lisat, lncRna, loci2path, locuszoomr, LOLA, LoomExperiment, LoopRig, lumi, 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, magpie, mariner, mCSEA, mCSEAdata, MDTS, MEAL, MEDIPS, megadepth, memes, metaseqR2, methInheritSim, MethReg, methrix, methylCC, methylInheritance, MethylSeekR, MethylSeqData, methylSig, methylumi, MinimumDistance, MIRA, missMethyl, mitoClone2, MitoHEAR, MMDiff2, mobileRNA, Modstrings, monaLisa, Moonlight2R, mosaics, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, MouseFM, MSA2dist, MultiAssayExperiment, multicrispr, MultiDataSet, multiHiCcompare, MungeSumstats, musicatk, MutSeqR, NanoMethViz, ncRNAtools, noisyr, NoRCE, normr, nucleR, nullranges, numbat, ocrRBBR, OGRE, oligoClasses, OmaDB, oncoPredict, openPrimeR, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, PACVr, pageRank, panelcn.mops, partCNV, PAST, pcaExplorer, peakCombiner, pepDat, pepStat, pgxRpi, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PhIPData, PICB, PIPETS, PlinkMatrix, plotgardener, plyinteractions, PopPsiSeqR, postNet, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, Pviz, QDNAseq, qpgraph, qsea, Qtlizer, R3CPET, R453Plus1Toolbox, raer, RAIDS, ramr, RapidoPGS, RareVariantVis, RBedMethyl, RCAS, rCGH, RcisTarget, recount, recount3, recountWorkflow, regionalpcs, regioneR, regionReport, regutools, REMP, RESOLVE, revert, rfPred, RgnTX, Rhisat2, RiboCrypt, RiboDiPA, RiboProfiling, rigvf, RiskyCNV, Rmmquant, rmspc, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAshapeQC, roar, RTCGAToolbox, saseR, SATS, scafari, scanMiR, scanMiRApp, scDblFinder, scmeth, scMultiome, scoreInvHap, scPipe, scPloidy, scRNAseq, scRNAseqApp, scruff, scuttle, segmenter, SEMPLR, seq2pathway, SeqArray, seqpac, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, sevenC, shinyepico, ShortRead, Signac, signeR, SigsPack, SimFFPE, SingleCellExperiment, sitadela, Site2Target, SMTrackR, snapcount, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SOMNiBUS, SparseSignatures, spatialLIBD, spatzie, SpectralTAD, SPICEY, SpliceImpactR, splicelogic, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, STADyUM, strandCheckR, syntenet, systemPipeR, TAPseq, target, TCGAbiolinks, TCGAutils, TCseq, TDbasedUFE, TDbasedUFEadv, TENET, TENET.AnnotationHub, TENET.ExperimentHub, TENxIO, tepr, TEQC, terraTCGAdata, TFARM, TFBSTools, TFEA.ChIP, TFHAZ, tidybulk, tidyCoverage, tLOH, TmCalculator, tracktables, transcriptR, transite, TRESS, tricycle, triplex, TumourMethData, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, Uniquorn, UPDhmm, VALERIE, VariantFiltering, VariantToolsData, VaSP, VCFArray, vmrseq, wiggleplotr, xcore, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, ZygosityPredictor
Suggests Me (71): AlphaMissenseR, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, AnnotationHub, autonomics, BeadArrayUseCases, biobroom, BiocGenerics, BiocParallel, CAGEWorkflow, CCAFE, Chicago, chicane, CNVScope, ComplexHeatmap, CTCF, cummeRbund, DFplyr, DGEobj, epivizrChart, GenomeInfoDb, GenomicState, GeuvadisTranscriptExpr, ggmanh, gkmSVM, Glimma, GSReg, GWASTools, HDF5Array, InteractiveComplexHeatmap, IRanges, iscream, iSEE, LACHESIS, lstar, maftools, MEDIPSData, MetaScope, methFuse, MiRaGE, MIRit, MoBPS, nanotubes, omicsPrint, parglms, polyRAD, recountmethylation, Rgff, rliger, RNAmodR.Data, RTCGA, S4Vectors, scGraphVerse, SeqGSEA, Seqinfo, seqmagick, Seurat, shiny.gosling, sigminer, Single.mTEC.Transcriptomes, smer, SNPassoc, splatter, systemPipeRdata, TFutils, universalmotif, updateObject, updog, valr, vectra, xcoredata