GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: Development (2.8)

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: Biocore Team c/o BioC user list

To install this package, start R and enter:

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

Documentation

PDF	R Script	Accessing Genome annotations from the UCSC Genome Browser
PDF	R Script	Making and Utilizing TranscriptDb Objects

Reference Manual

Details

biocViews	Genetics, Infrastructure, Annotation, HighThroughputSequencing
Depends	IRanges, GenomicRanges
Imports	methods, DBI, RSQLite, IRanges, GenomicRanges, Biostrings, rtracklayer, biomaRt, RCurl, utils
Suggests	rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18, RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me	Biostrings, GenomicRanges, Rsamtools, chipseq
Version	1.3.15

Package Downloads

Package Source	GenomicFeatures_1.3.15.tar.gz
Windows Binary	GenomicFeatures_1.3.15.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicFeatures_1.3.15.tgz
Package Downloads Report	Download Stats