GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: Development (3.0)

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. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence

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

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GenomicFeatures")

To cite this package in a publication, start R and enter:

    citation("GenomicFeatures")

Documentation

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

Details

biocViews Annotation, Genetics, Infrastructure, Sequencing, Software
Version 1.17.0
In Bioconductor since BioC 2.5 (R-2.10)
License Artistic-2.0
Depends BiocGenerics(>= 0.1.0), IRanges(>= 1.17.13), GenomicRanges(>= 1.15.25), AnnotationDbi(>= 1.25.7)
Imports methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), Biostrings(>= 2.23.2), rtracklayer(>= 1.15.1), biomaRt(>= 2.17.1), RCurl, utils, Biobase(>= 2.15.1), GenomeInfoDb
Suggests org.Mm.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), 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.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene(>= 2.7.1), Rsamtools, pasillaBamSubset(>= 0.0.5), seqnames.db, RUnit, BiocStyle, knitr
System Requirements
URL
Depends On Me exomePeak, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, ggtut, Homo.sapiens, Mus.musculus, OrganismDbi, Rattus.norvegicus, SplicingGraphs, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Athaliana.BioMart.plantsmart19, TxDb.Athaliana.BioMart.plantsmart21, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
Imports Me AllelicImbalance, biovizBase, casper, ChIPpeakAnno, ChIPseeker, CompGO, customProDB, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, geneLenDataBase, ggbio, gmapR, Gviz, Homo.sapiens, HTSeqGenie, lumi, MEDIPS, methyAnalysis, Mus.musculus, QuasR, Rattus.norvegicus, SplicingGraphs, trackViewer, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Athaliana.BioMart.plantsmart19, TxDb.Athaliana.BioMart.plantsmart21, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, VariantAnnotation, VariantTools
Suggests Me biomvRCNS, Biostrings, chipseq, DESeq2, DEXSeq, easyRNASeq, GenomicAlignments, GenomicRanges, ggtut, ind1KG, MiRaGE, parathyroidSE, RIPSeeker, Rsamtools, ShortRead

Package Downloads

Package Source GenomicFeatures_1.17.0.tar.gz
Windows Binary GenomicFeatures_1.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicFeatures_1.17.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center