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Bioconductor - GenomicFeatures (development version)

GenomicFeatures

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

Query the gene models of a given organism/assembly

Bioconductor version: Development (3.22)

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

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 "4.5") 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 1.61.4 In Bioconductor since BioC 2.5 (R-2.10) (15.5 years) License Artistic-2.0 Depends R (>= 3.5.0), BiocGenerics(>= 0.51.2), S4Vectors(>= 0.17.29), IRanges(>= 2.37.1), Seqinfo, GenomicRanges(>= 1.61.1), AnnotationDbi(>= 1.41.4) Imports methods, utils, stats, DBI, XVector, Biostrings(>= 2.77.2), rtracklayer(>= 1.69.1) System Requirements URL https://bioconductor.org/packages/GenomicFeatures Bug Reports https://github.com/Bioconductor/GenomicFeatures/issues See More Suggests GenomeInfoDb, txdbmaker, 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), 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 Linking To Enhances Depends On Me Cogito, cpvSNP, CRISPRseek, ensembldb, GSReg, Guitar, HelloRanges, mygene, OrganismDbi, OUTRIDER, RareVariantVis, RiboDiPA, SplicingGraphs, txdbmaker, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, Homo.sapiens, Mus.musculus, Rattus.norvegicus, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Athaliana.BioMart.plantsmart28, TxDb.Athaliana.BioMart.plantsmart51, TxDb.Btaurus.UCSC.bosTau8.refGene, TxDb.Btaurus.UCSC.bosTau9.refGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Celegans.UCSC.ce11.refGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Cfamiliaris.UCSC.canFam3.refGene, TxDb.Cfamiliaris.UCSC.canFam4.refGene, TxDb.Cfamiliaris.UCSC.canFam5.refGene, TxDb.Cfamiliaris.UCSC.canFam6.refGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Drerio.UCSC.danRer11.refGene, TxDb.Ggallus.UCSC.galGal4.refGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Ggallus.UCSC.galGal6.refGene, TxDb.Hsapiens.BioMart.igis, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg38.refGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, TxDb.Mmulatta.UCSC.rheMac3.refGene, TxDb.Mmulatta.UCSC.rheMac8.refGene, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Ptroglodytes.UCSC.panTro4.refGene, TxDb.Ptroglodytes.UCSC.panTro5.refGene, TxDb.Ptroglodytes.UCSC.panTro6.refGene, TxDb.Rnorvegicus.BioMart.igis, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, TxDb.Sscrofa.UCSC.susScr11.refGene, TxDb.Sscrofa.UCSC.susScr3.refGene, generegulation Imports Me AllelicImbalance, AnnotationHubData, annotatr, APAlyzer, appreci8R, ASpli, atena, bambu, BgeeCall, BindingSiteFinder, biovizBase, bumphunter, BUSpaRse, CAGEfightR, CAGEr, casper, chevreulProcess, ChIPpeakAnno, ChIPQC, ChIPseeker, consensusDE, crisprDesign, crisprViz, crupR, CSSQ, customProDB, Damsel, decompTumor2Sig, derfinder, derfinderPlot, DNAfusion, doubletrouble, EDASeq, ELMER, ELViS, EpiMix, epimutacions, EpiTxDb, epivizrData, epivizrStandalone, esATAC, EventPointer, factR, FindIT2, FLAMES, FRASER, GA4GHshiny, gDNAx, geneAttribution, GenomicInteractionNodes, GenomicPlot, GenVisR, ggbio, gINTomics, gmapR, gmoviz, goseq, GUIDEseq, Gviz, gwascat, HiLDA, icetea, InPAS, INSPEcT, IntEREst, karyoploteR, lumi, magpie, mCSEA, metaseqR2, methylumi, msgbsR, multicrispr, musicatk, ORFik, Organism.dplyr, OutSplice, proActiv, proBAMr, ProteoDisco, PureCN, qpgraph, QuasR, raer, RCAS, recoup, RgnTX, rGREAT, RiboCrypt, RiboProfiling, ribosomeProfilingQC, RITAN, RNAmodR, SARC, saseR, scanMiRApp, scruff, SGSeq, sitadela, spatzie, SPLINTER, srnadiff, StructuralVariantAnnotation, svaNUMT, svaRetro, TAPseq, TCGAutils, TFEA.ChIP, trackViewer, transcriptR, transmogR, TRESS, txcutr, tximeta, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, GenomicState, Homo.sapiens, Mus.musculus, Rattus.norvegicus, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Hsapiens.BioMart.igis, TxDb.Rnorvegicus.BioMart.igis, DMRcatedata, geneLenDataBase, GenomicDistributionsData, scRNAseq, ExpHunterSuite, CSeQTL, driveR, HiCociety, MAAPER, oncoPredict Suggests Me BANDITS, biomvRCNS, Biostrings, BSgenomeForge, chipseq, chromPlot, CrispRVariants, csaw, cummeRbund, DEXSeq, eisaR, fishpond, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, HDF5Array, HiContacts, InteractiveComplexHeatmap, IRanges, MiRaGE, MutationalPatterns, pageRank, plotgardener, recount, RNAmodR.ML, Rsamtools, rtracklayer, scPipe, Seqinfo, ShortRead, SummarizedExperiment, systemPipeR, TFutils, tidyCoverage, TnT, VplotR, wiggleplotr, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau8, BSgenome.Btaurus.UCSC.bosTau9, BSgenome.Celegans.UCSC.ce10, BSgenome.Celegans.UCSC.ce11, BSgenome.Celegans.UCSC.ce2, BSgenome.Cfamiliaris.UCSC.canFam2, BSgenome.Cfamiliaris.UCSC.canFam3, BSgenome.Dmelanogaster.UCSC.dm2, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Drerio.UCSC.danRer11, BSgenome.Drerio.UCSC.danRer5, BSgenome.Drerio.UCSC.danRer6, BSgenome.Drerio.UCSC.danRer7, BSgenome.Gaculeatus.UCSC.gasAcu1, BSgenome.Ggallus.UCSC.galGal3, BSgenome.Ggallus.UCSC.galGal4, BSgenome.Hsapiens.UCSC.hg17, BSgenome.Mmulatta.UCSC.rheMac2, BSgenome.Mmulatta.UCSC.rheMac3, BSgenome.Mmusculus.UCSC.mm8, BSgenome.Ptroglodytes.UCSC.panTro2, BSgenome.Ptroglodytes.UCSC.panTro3, BSgenome.Rnorvegicus.UCSC.rn6, BioPlex, curatedAdipoChIP, ObMiTi, Single.mTEC.Transcriptomes, systemPipeRdata, CAGEWorkflow, polyRAD Links To Me Build Report Build Report Package Archives

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