To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.14

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>

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

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, Infrastructure, Sequencing, Software
Version 1.16.3
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 Archives

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

Package Source GenomicFeatures_1.16.3.tar.gz
Windows Binary GenomicFeatures_1.16.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicFeatures_1.16.3.tgz
Mac OS X 10.9 (Mavericks) GenomicFeatures_1.16.3.tgz
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