GenomicFeatures

DOI: 10.18129/B9.bioc.GenomicFeatures    

Tools for making and manipulating transcript centric annotations

Bioconductor version: Release (3.8)

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, H. Pag├Ęs, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence, V. Obenchain

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicFeatures")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GenomicFeatures", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicFeatures")

 

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

Details

biocViews Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.34.1
In Bioconductor since BioC 2.5 (R-2.10) (9 years)
License Artistic-2.0
Depends BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.13.23), GenomeInfoDb(>= 1.15.4), 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), rtracklayer(>= 1.39.7), 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.ce2, BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene(>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset(>= 0.0.5), GenomicAlignments(>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me cpvSNP, ensembldb, exomePeak, 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, InPAS, IVAS, Mus.musculus, mygene, OrganismDbi, OUTRIDER, RareVariantVis, Rattus.norvegicus, RNAprobR, rnaseqGene, SplicingGraphs, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Athaliana.BioMart.plantsmart28, TxDb.Btaurus.UCSC.bosTau8.refGene, TxDb.Celegans.UCSC.ce11.refGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Cfamiliaris.UCSC.canFam3.refGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Ggallus.UCSC.galGal4.refGene, TxDb.Ggallus.UCSC.galGal5.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.Mmulatta.UCSC.rheMac3.refGene, TxDb.Mmulatta.UCSC.rheMac8.refGene, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Ptroglodytes.UCSC.panTro4.refGene, TxDb.Ptroglodytes.UCSC.panTro5.refGene, TxDb.Rnorvegicus.BioMart.igis, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.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, appreci8R, ASpli, BiocOncoTK, biovizBase, bumphunter, CAGEfightR, casper, ChIPpeakAnno, ChIPQC, ChIPseeker, compEpiTools, CompGO, consensusDE, crisprseekplus, csaw, customProDB, derfinder, derfinderPlot, EDASeq, ELMER, epivizrData, epivizrStandalone, esATAC, EventPointer, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, GA4GHshiny, genbankr, geneAttribution, geneLenDataBase, GenVisR, ggbio, gmapR, gQTLstats, Gviz, gwascat, Homo.sapiens, HTSeqGenie, icetea, INSPEcT, IntEREst, karyoploteR, lumi, mCSEA, metagene, methyAnalysis, msgbsR, MTseeker, MTseekerData, Mus.musculus, ORFik, Organism.dplyr, PGA, proBAMr, PureCN, qpgraph, QuasR, Rattus.norvegicus, RCAS, rCGH, RiboProfiling, scruff, SGSeq, SplicingGraphs, SPLINTER, srnadiff, systemPipeR, TCGAbiolinks, TCGAutils, TFEA.ChIP, trackViewer, transcriptR, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Hsapiens.BioMart.igis, TxDb.Rnorvegicus.BioMart.igis, tximeta, Ularcirc, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR
Suggests Me AnnotationHub, biomvRCNS, Biostrings, BSgenome.Btaurus.UCSC.bosTau3, BSgenome.Btaurus.UCSC.bosTau4, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Btaurus.UCSC.bosTau8, 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.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, chipseq, chromPlot, CrispRVariants, cummeRbund, DEXSeq, flipflop, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, IRanges, MiRaGE, parathyroidSE, recount, RIPSeeker, Rsamtools, rtracklayer, ShortRead, Single.mTEC.Transcriptomes, SummarizedExperiment, TFutils, TnT, wiggleplotr
Links To Me
Build Report  

Package Archives

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

Source Package GenomicFeatures_1.34.1.tar.gz
Windows Binary GenomicFeatures_1.34.1.zip
Mac OS X 10.11 (El Capitan) GenomicFeatures_1.34.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicFeatures
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicFeatures
Package Short Url http://bioconductor.org/packages/GenomicFeatures/
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