This is the released version of GenomicFeatures; for the devel version, seeGenomicFeatures .
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")):
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 .
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicFeatures")
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 , cpvSNP , 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 , ChIPpeakAnno , ChIPQC , ChIPseeker , compEpiTools , consensusDE , crisprDesign , crisprViz , CSSQ , customProDB , Damsel , decompTumor2Sig , derfinder , derfinderPlot , DNAfusion , doubletrouble , EDASeq , ELMER , 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 , 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 , driveR , MAAPER , MOCHA , oncoPredict , SeedMatchR
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 , 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 , parathyroidSE , Single.mTEC.Transcriptomes , systemPipeRdata , CAGEWorkflow , polyRAD
Links To Me
Build Report
Build Report
Follow Installation instructions to use this package in your R session.