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

GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

source("http://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")

 

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

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Infrastructure, Software
Version	1.14.5
In Bioconductor since	BioC 2.5 (R-2.10)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.1.0), IRanges(>= 1.17.13), GenomicRanges(>= 1.13.16), AnnotationDbi(>= 1.23.14)
Imports	methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings(>= 2.23.2), rtracklayer(>= 1.15.1), biomaRt(>= 2.17.1), RCurl, utils, Biobase(>= 2.15.1)
Suggests	rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, 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
System Requirements
URL
Depends On Me	ChIPpeakAnno, 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.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, 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, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Athaliana.BioMart.plantsmart19, 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, DEXSeq, easyRNASeq, GenomicRanges, ggtut, Gviz, HTSeqGenie, ind1KG, MiRaGE, parathyroidSE, RIPSeeker, Rsamtools, ShortRead

Package Archives

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

Package Source	GenomicFeatures_1.14.5.tar.gz
Windows Binary	GenomicFeatures_1.14.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicFeatures_1.14.5.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats