GenomicFeatures
DOI:
10.18129/B9.bioc.GenomicFeatures
Tools for making and manipulating transcript centric annotations
Bioconductor version: Release (3.6)
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. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R,
enter citation("GenomicFeatures")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("GenomicFeatures")
Details
| biocViews |
Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.30.3 |
| In Bioconductor since |
BioC 2.5 (R-2.10) (8.5 years) |
| License |
Artistic-2.0 |
| Depends |
BiocGenerics(>= 0.1.0), S4Vectors(>= 0.9.47), IRanges(>= 2.11.16), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.29.14), AnnotationDbi(>= 1.33.15) |
| Imports |
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RMySQL, RCurl, XVector, Biostrings(>= 2.23.3), rtracklayer(>= 1.29.24), biomaRt(>= 2.17.1), Biobase(>= 2.15.1) |
| LinkingTo |
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| Suggests |
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.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset(>= 0.0.5), GenomicAlignments, ensembldb, RUnit, BiocStyle, knitr |
| SystemRequirements |
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| Enhances |
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| URL |
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| 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, GSReg, Guitar, HelloRanges, Homo.sapiens, IMAS, InPAS, IVAS, Mus.musculus, mygene, OrganismDbi, RareVariantVis, Rattus.norvegicus, RNAprobR, 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.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.susScr3.refGene |
| Imports Me |
AllelicImbalance, alpine, AnnotationHubData, annotatr, ASpli, biovizBase, bumphunter, casper, ChIPpeakAnno, ChIPQC, ChIPseeker, compEpiTools, CompGO, 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, INSPEcT, IntEREst, lumi, metagene, methyAnalysis, msgbsR, Mus.musculus, Organism.dplyr, PGA, proBAMr, PureCN, qpgraph, QuasR, Rattus.norvegicus, RCAS, rCGH, RiboProfiling, SGSeq, SplicingGraphs, SPLINTER, systemPipeR, TCGAbiolinks, trackViewer, transcriptR, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Athaliana.BioMart.plantsmart25, TxDb.Hsapiens.BioMart.igis, TxDb.Rnorvegicus.BioMart.igis, 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, easyRNASeq, flipflop, GenomeInfoDb, GenomicAlignments, GenomicRanges, groHMM, IRanges, MiRaGE, parathyroidSE, recount, RIPSeeker, Rsamtools, rtracklayer, ShortRead, Single.mTEC.Transcriptomes, SummarizedExperiment, TnT, wiggleplotr |
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