GenomicFeatures
DOI:
10.18129/B9.bioc.GenomicFeatures
This is the development version of GenomicFeatures; for the stable release version, see
GenomicFeatures.
Conveniently import and query gene models
Bioconductor version: Development (3.17)
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 [aut], H. Pagès [aut, cre], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], D. Sarkar [aut], M. Lawrence [aut], V. Obenchain [aut], S. Arora [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], P. Shannon [ctb], L. Shepherd [ctb], D. Tenenbaum [ctb], D. Van Twisk [ctb]
Maintainer: H. Pagès <hpages.on.github at gmail.com>
Citation (from within R,
enter citation("GenomicFeatures")
):
Installation
To install this package, start R (version
"4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GenomicFeatures")
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("GenomicFeatures")
Details
biocViews |
Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
Version |
1.51.0 |
In Bioconductor since |
BioC 2.5 (R-2.10) (13 years) |
License |
Artistic-2.0 |
Depends |
R (>= 3.5.0), BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.13.23), GenomeInfoDb(>= 1.25.7), GenomicRanges(>= 1.31.17), AnnotationDbi(>= 1.41.4) |
Imports |
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector(>= 0.19.7), Biostrings(>= 2.47.6), BiocIO, rtracklayer(>= 1.51.5), biomaRt(>= 2.17.1), Biobase(>= 2.15.1) |
LinkingTo |
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Suggests |
RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset(>= 0.0.5), GenomicAlignments(>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown |
SystemRequirements |
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Enhances |
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URL |
https://bioconductor.org/packages/GenomicFeatures |
BugReports |
https://github.com/Bioconductor/GenomicFeatures/issues |
Depends On Me |
Cogito, cpvSNP, ensembldb, generegulation, GSReg, Guitar, HelloRanges, IMAS, IVAS, mygene, OrganismDbi, OUTRIDER, RareVariantVis, RiboDiPA, SplicingGraphs |
Imports Me |
AllelicImbalance, alpine, AnnotationHubData, annotatr, APAlyzer, appreci8R, ASpediaFI, ASpli, ATACCoGAPS, bambu, BgeeCall, BiocOncoTK, biovizBase, bumphunter, BUSpaRse, CAGEfightR, casper, ChIPpeakAnno, ChIPQC, ChIPseeker, compEpiTools, consensusDE, crisprDesign, crisprseekplus, crisprViz, CSSQ, customProDB, dasper, decompTumor2Sig, DegNorm, derfinder, derfinderPlot, DMRcatedata, EDASeq, ELMER, EpiMix, epimutacions, EpiTxDb, epivizrData, epivizrStandalone, esATAC, EventPointer, exomePeak2, factR, FindIT2, FLAMES, FRASER, GA4GHshiny, genbankr, geneAttribution, geneLenDataBase, GenomicDistributionsData, GenomicInteractionNodes, GenVisR, ggbio, gmapR, gmoviz, GUIDEseq, Gviz, gwascat, HiLDA, HTSeqGenie, icetea, InPAS, INSPEcT, IntEREst, karyoploteR, lumi, mCSEA, metagene, metaseqR2, methylumi, msgbsR, multicrispr, musicatk, NoRCE, ORFik, Organism.dplyr, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, qpgraph, QuasR, RCAS, rCGH, recoup, RgnTX, rGREAT, Rhisat2, RiboCrypt, RiboProfiling, ribosomeProfilingQC, RITAN, RLSeq, RNAmodR, scanMiRApp, scPipe, scRNAseq, scruff, SGSeq, sitadela, spatzie, SplicingGraphs, SPLINTER, srnadiff, StructuralVariantAnnotation, svaNUMT, svaRetro, TAPseq, TCGAutils, TFEA.ChIP, trackViewer, transcriptR, TRESS, txcutr, tximeta, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR |
Suggests Me |
AnnotationHub, BANDITS, biomvRCNS, BioPlex, Biostrings, CAGEWorkflow, chipseq, chromPlot, CrispRVariants, csaw, cummeRbund, curatedAdipoChIP, DEXSeq, eisaR, fishpond, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, HDF5Array, InteractiveComplexHeatmap, IRanges, MiRaGE, MutationalPatterns, ObMiTi, ODER, pageRank, parathyroidSE, plotgardener, recount, RNAmodR.ML, Rsamtools, rtracklayer, ShortRead, Single.mTEC.Transcriptomes, SummarizedExperiment, systemPipeR, systemPipeRdata, TFutils, TnT, VplotR, wiggleplotr |
Links To Me |
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Build Report |
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Package Archives
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