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

Tools for making and manipulating transcript centric annotations

Bioconductor version: Development (3.5)

A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

Author: M. Carlson, H. Pag├Ęs, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at>

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PDF R Script Making and Utilizing TxDb Objects
PDF   Reference Manual
Text   NEWS


biocViews Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 2.5 (R-2.10) (7 years)
License Artistic-2.0
Depends BiocGenerics(>= 0.1.0), S4Vectors(>= 0.9.47), IRanges(>= 2.3.21), GenomeInfoDb(>= 1.5.16), GenomicRanges(>= 1.21.32), AnnotationDbi(>= 1.33.15)
Imports methods, utils, stats, tools, DBI, RSQLite, RCurl, XVector, Biostrings(>= 2.23.3), rtracklayer(>= 1.29.24), biomaRt(>= 2.17.1), Biobase(>= 2.15.1)
Suggests,, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments, RUnit, BiocStyle, knitr
Depends On Me ASpli, cpvSNP, ensembldb, exomePeak, Guitar, HelloRanges, InPAS, IVAS, mygene, RNAprobR, SplicingGraphs
Imports Me AllelicImbalance, alpine, AnnotationHubData, annotatr, biovizBase, bumphunter, casper, ChIPpeakAnno, ChIPQC, ChIPseeker, compEpiTools, CompGO, crisprseekplus, csaw, customProDB, derfinder, derfinderPlot, EDASeq, ELMER, epivizrData, epivizrStandalone, genbankr, geneAttribution, GenVisR, ggbio, gmapR, gQTLstats, Gviz, gwascat, HTSeqGenie, INSPEcT, metagene, methyAnalysis, PGA, proBAMr, qpgraph, QuasR, RCAS, rCGH, SGSeq, SplicingGraphs, SPLINTER, systemPipeR, TCGAbiolinks, trackViewer, transcriptR, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR
Suggests Me AnnotationHub, biomvRCNS, Biostrings, chipseq, chromPlot, CrispRVariants, cummeRbund, DEXSeq, easyRNASeq, flipflop, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, IRanges, MiRaGE, recount, RIPSeeker, Rsamtools, ShortRead, SummarizedExperiment
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