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 (3.21)
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")| Obtaining and Utilizing TxDb Objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.59.0 |
| 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_1.59.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |