GenomicFeatures

DOI: 10.18129/B9.bioc.GenomicFeatures  

Conveniently import and query gene models

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.52.2
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)
LinkingTo
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
Enhances
URL	https://bioconductor.org/packages/GenomicFeatures
BugReports	https://github.com/Bioconductor/GenomicFeatures/issues
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, 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, 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, ODER, 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_1.52.2.tar.gz
Windows Binary	GenomicFeatures_1.52.2.zip
macOS Binary (x86_64)	GenomicFeatures_1.52.2.tgz
macOS Binary (arm64)	GenomicFeatures_1.52.2.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
Old Source Packages for BioC 3.17	Source Archive