Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
To view documentation for the version of this package installed
in your system, start R and enter:
biocViews |
Annotation, DataImport, Software, Visualization |
Version |
1.52.1 |
In Bioconductor since |
BioC 2.2 (R-2.7) (13.5 years) |
License |
Artistic-2.0 + file LICENSE |
Depends |
R (>= 3.3), methods, GenomicRanges(>= 1.37.2) |
Imports |
XML (>= 1.98-0), BiocGenerics(>= 0.35.3), S4Vectors(>= 0.23.18), IRanges(>= 2.13.13), XVector(>= 0.19.7), GenomeInfoDb(>= 1.15.2), Biostrings(>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) |
LinkingTo |
S4Vectors, IRanges, XVector |
Suggests |
BSgenome(>= 1.33.4), humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit |
SystemRequirements |
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Enhances |
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URL |
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Depends On Me |
BRGenomics, BSgenome, CAGEfightR, ChIPComp, ChIPSeqSpike, CoverageView, CSSQ, cummeRbund, EatonEtAlChIPseq, ExCluster, geneXtendeR, GenomicFiles, groHMM, Guitar, HelloRanges, IdeoViz, liftOver, MethylSeekR, ORFhunteR, r3Cseq, sequencing, StructuralVariantAnnotation |
Imports Me |
ALPS, AnnotationHubData, annotatr, APAlyzer, ASpediaFI, ATACseqQC, ballgown, BgeeCall, biscuiteer, BiSeq, branchpointer, BSgenome, CAGEr, casper, CexoR, ChIPanalyser, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPseeker, ChromHeatMap, ChromSCape, chromswitch, circRNAprofiler, CNEr, coMET, compartmap, CompGO, consensusSeekeR, contiBAIT, conumee, customProDB, DeepBlueR, derfinder, DEScan2, diffHic, diffloop, diffUTR, DMCFB, DMCHMM, DMRcatedata, dmrseq, ELMER, ENCODExplorer, enrichTF, ensembldb, epidecodeR, epigraHMM, erma, esATAC, exomePeak2, fcScan, genbankr, geneAttribution, geneLenDataBase, GeneStructureTools, genomation, GenomicFeatures, GenomicInteractions, GenomicState, genotypeeval, ggbio, gmapR, gmoviz, GOTHiC, GreyListChIP, Gviz, hiAnnotator, HiCDCPlus, HiTC, HTSeqGenie, icetea, igvR, INSPEcT, InTAD, IsoformSwitchAnalyzeR, karyoploteR, MACPET, MADSEQ, maser, MEDIPS, metagene, metagene2, metaseqR2, methrix, methyAnalysis, methylKit, motifbreakR, MotifDb, multicrispr, NADfinder, nanotatoR, nearBynding, NoRCE, normr, OMICsPCA, ORFik, PAST, periodicDNA, plyranges, pram, primirTSS, proBAMr, profileplyr, PureCN, qsea, QuasR, RCAS, recount, recount3, recoup, regioneR, REMP, Repitools, RGMQL, RiboProfiling, ribosomeProfilingQC, RIPAT, RNAmodR, RNAprobR, roar, SCANVIS, scPipe, scruff, seqCAT, seqplots, seqsetvis, sevenC, SGSeq, shinyepico, SigsPack, SingscoreAMLMutations, sitadela, soGGi, srnadiff, systemPipeRdata, TFBSTools, trackViewer, transcriptR, tRNAscanImport, TSRchitect, VariantAnnotation, VariantTools, wavClusteR, wiggleplotr |
Suggests Me |
alpine, AnnotationHub, autonomics, BiocFileCache, biovizBase, bsseq, chipseqDB, cicero, CINdex, compEpiTools, CrispRVariants, DAMEfinder, dasper, dsQTL, eisaR, EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3, epivizrChart, epivizrData, FDb.FANTOM4.promoters.hg19, geneXtendeR, GenomicAlignments, GenomicDistributions, GenomicRanges, GeuvadisTranscriptExpr, goseq, gwascat, InPAS, interactiveDisplay, megadepth, methylumi, miRBaseConverter, MutationalPatterns, nanotubes, OrganismDbi, PasillaTranscriptExpr, Pi, PICS, PING, pipeFrame, pqsfinder, R453Plus1Toolbox, RcisTarget, rGADEM, Ringo, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RnBeads, RSVSim, signeR, similaRpeak, spatialLIBD, SynExtend, TAPseq, TCGAutils, triplex, tRNAdbImport, TVTB |
Links To Me |
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Build Report |
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