To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")

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

GenomicFeatures

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see GenomicFeatures.

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.12

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:

## 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")

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

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Infrastructure, Software
Version	1.12.4
In Bioconductor since	BioC 2.5 (R-2.10) (6.5 years)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.1.0), IRanges(>= 1.17.13), GenomicRanges(>= 1.11.11), AnnotationDbi(>= 1.19.36)
Imports	methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings(>= 2.23.2), rtracklayer(>= 1.15.1), biomaRt, RCurl, utils, Biobase(>= 2.15.1)
LinkingTo
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), RUnit
SystemRequirements
Enhances
URL
Depends On Me	ChIPpeakAnno, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, ggtut, Homo.sapiens, IlluminaHumanMethylation450kprobe, Mus.musculus, OrganismDbi, Rattus.norvegicus, SplicingGraphs, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, 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	biovizBase, casper, ChIPpeakAnno, 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, 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.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, RIPSeeker, Rsamtools, ShortRead
Build Report

Package Archives

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

Package Source	GenomicFeatures_1.12.4.tar.gz
Windows Binary	GenomicFeatures_1.12.4.zip
Mac OS X 10.6 (Snow Leopard)	GenomicFeatures_1.12.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/GenomicFeatures/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/GenomicFeatures/
Package Downloads Report	Download Stats

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