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GenomicFeatures

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

Conveniently import and query gene models

Bioconductor version: Development (3.18)

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

Details

biocViews Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.53.1
In Bioconductor since BioC 2.5 (R-2.10) (14 years)
License Artistic-2.0
Depends R (>= 3.5.0), BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.13.23), GenomeInfoDb(>= 1.35.8), 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)
Linking To
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
System Requirements
Enhances
URL https://bioconductor.org/packages/GenomicFeatures
Bug Reports https://github.com/Bioconductor/GenomicFeatures/issues
See More
Depends On Me Cogito, cpvSNP, ensembldb, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, generegulation, GSReg, Guitar, HelloRanges, Homo.sapiens, IMAS, IVAS, Mus.musculus, mygene, OrganismDbi, OUTRIDER, RareVariantVis, Rattus.norvegicus, RiboDiPA, SplicingGraphs, 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
Imports Me AllelicImbalance, AnnotationHubData, annotatr, APAlyzer, appreci8R, ASpli, ATACCoGAPS, bambu, BgeeCall, BindingSiteFinder, BiocOncoTK, biovizBase, bumphunter, BUSpaRse, CAGEfightR, casper, ChIPpeakAnno, ChIPQC, ChIPseeker, compEpiTools, consensusDE, crisprDesign, crisprseekplus, crisprViz, CSSQ, customProDB, decompTumor2Sig, DegNorm, derfinder, derfinderPlot, DMRcatedata, DNAfusion, EDASeq, ELMER, EpiMix, epimutacions, EpiTxDb, epivizrData, epivizrStandalone, esATAC, EventPointer, exomePeak2, factR, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, FindIT2, FLAMES, FRASER, GA4GHshiny, genbankr, geneAttribution, geneLenDataBase, GenomicDistributionsData, GenomicInteractionNodes, GenomicState, GenVisR, ggbio, gmapR, gmoviz, GUIDEseq, Gviz, gwascat, HiLDA, Homo.sapiens, HTSeqGenie, icetea, InPAS, INSPEcT, IntEREst, karyoploteR, lumi, magpie, mCSEA, metagene, metaseqR2, methylumi, msgbsR, multicrispr, Mus.musculus, musicatk, NoRCE, ORFik, Organism.dplyr, OutSplice, proActiv, proBAMr, profileplyr, ProteoDisco, PureCN, qpgraph, QuasR, Rattus.norvegicus, RCAS, rCGH, recoup, RgnTX, rGREAT, Rhisat2, RiboCrypt, RiboProfiling, ribosomeProfilingQC, RITAN, RLSeq, RNAmodR, scanMiRApp, scRNAseq, scruff, SGSeq, sitadela, spatzie, SplicingGraphs, SPLINTER, srnadiff, StructuralVariantAnnotation, svaNUMT, svaRetro, TAPseq, TCGAutils, TFEA.ChIP, trackViewer, transcriptR, TRESS, txcutr, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Hsapiens.BioMart.igis, TxDb.Rnorvegicus.BioMart.igis, tximeta, Ularcirc, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR
Suggests Me AnnotationHub, BANDITS, biomvRCNS, BioPlex, Biostrings, 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, BSgenomeForge, CAGEWorkflow, chipseq, chromPlot, CrispRVariants, csaw, cummeRbund, curatedAdipoChIP, DEXSeq, eisaR, fishpond, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, HDF5Array, HiContacts, InteractiveComplexHeatmap, IRanges, MiRaGE, MutationalPatterns, ObMiTi, pageRank, parathyroidSE, plotgardener, recount, RNAmodR.ML, Rsamtools, rtracklayer, scPipe, ShortRead, Single.mTEC.Transcriptomes, SummarizedExperiment, systemPipeR, systemPipeRdata, TFutils, TnT, VplotR, wiggleplotr
Links To Me
Build Report  

Package Archives

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

Source Package GenomicFeatures_1.53.1.tar.gz
Windows Binary GenomicFeatures_1.53.1.zip
macOS Binary (x86_64) GenomicFeatures_1.53.1.tgz
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