GenomicFeatures

Query the gene models of a given organism/assembly


Bioconductor version: Release (3.20)

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")
Obtaining and Utilizing TxDb Objects HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.58.0
In Bioconductor since BioC 2.5 (R-2.10) (15 years)
License Artistic-2.0
Depends R (>= 3.5.0), BiocGenerics(>= 0.51.2), S4Vectors(>= 0.17.29), IRanges(>= 2.37.1), GenomeInfoDb(>= 1.35.8), GenomicRanges(>= 1.55.2), AnnotationDbi(>= 1.41.4)
Imports methods, utils, stats, DBI, XVector, Biostrings, rtracklayer
System Requirements
URL https://bioconductor.org/packages/GenomicFeatures
Bug Reports https://github.com/Bioconductor/GenomicFeatures/issues
See More
Suggests 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), 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
Linking To
Enhances
Depends On Me Cogito, GSReg, Guitar, HelloRanges, OUTRIDER, OrganismDbi, RareVariantVis, RiboDiPA, SplicingGraphs, cpvSNP, ensembldb, mygene, 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 APAlyzer, ASpli, AllelicImbalance, AnnotationHubData, BUSpaRse, BgeeCall, BindingSiteFinder, CAGEfightR, CAGEr, CSSQ, ChIPQC, ChIPpeakAnno, ChIPseeker, DNAfusion, Damsel, EDASeq, ELMER, EpiMix, EpiTxDb, EventPointer, FLAMES, FRASER, FindIT2, GA4GHshiny, GUIDEseq, GenVisR, GenomicInteractionNodes, GenomicPlot, Gviz, HiLDA, INSPEcT, InPAS, IntEREst, ORFik, Organism.dplyr, OutSplice, ProteoDisco, PureCN, QuasR, RCAS, RITAN, RNAmodR, RgnTX, RiboCrypt, RiboProfiling, SARC, SGSeq, SPLINTER, StructuralVariantAnnotation, TAPseq, TCGAutils, TFEA.ChIP, TRESS, UMI4Cats, Ularcirc, VariantAnnotation, VariantFiltering, VariantTools, annotatr, appreci8R, atena, bambu, biovizBase, bumphunter, casper, compEpiTools, consensusDE, crisprDesign, crisprViz, customProDB, decompTumor2Sig, derfinderPlot, derfinder, doubletrouble, epimutacions, epivizrData, epivizrStandalone, esATAC, factR, gDNAx, gINTomics, geneAttribution, ggbio, gmapR, gmoviz, goseq, gwascat, icetea, karyoploteR, lumi, magpie, metaseqR2, methylumi, msgbsR, multicrispr, musicatk, proActiv, proBAMr, qpgraph, rGREAT, raer, recoup, ribosomeProfilingQC, saseR, scanMiRApp, scruff, sitadela, spatzie, svaNUMT, svaRetro, trackViewer, transcriptR, transmogR, txcutr, tximeta, 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, driveR, MAAPER, MOCHA, oncoPredict, SeedMatchR
Suggests Me BANDITS, BSgenomeForge, Biostrings, CrispRVariants, DEXSeq, GenomeInfoDb, GenomicAlignments, GenomicRanges, HDF5Array, HiContacts, IRanges, InteractiveComplexHeatmap, MiRaGE, MutationalPatterns, RNAmodR.ML, Rsamtools, ShortRead, SummarizedExperiment, TFutils, TnT, VplotR, biomvRCNS, chipseq, chromPlot, csaw, cummeRbund, eisaR, fishpond, pageRank, plotgardener, recount, rtracklayer, scPipe, systemPipeR, tidyCoverage, 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, parathyroidSE, Single.mTEC.Transcriptomes, systemPipeRdata, CAGEWorkflow, polyRAD
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GenomicFeatures_1.58.0.tar.gz
Windows Binary (x86_64) GenomicFeatures_1.58.0.zip
macOS Binary (x86_64) GenomicFeatures_1.58.0.tgz
macOS Binary (arm64) GenomicFeatures_1.57.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicFeatures
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicFeatures
Bioc Package Browser https://code.bioconductor.org/browse/GenomicFeatures/
Package Short Url https://bioconductor.org/packages/GenomicFeatures/
Package Downloads Report Download Stats