GenomicFeatures

Tools for making and manipulating transcript centric annotations

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

Documentation

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

Details

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

Package Downloads

Package source	GenomicFeatures_1.0.10.tar.gz
Windows 32-bit binary	GenomicFeatures_1.0.10.zip
Windows 64-bit binary	GenomicFeatures_1.0.10.zip
MacOS X 10.5 (Leopard) binary	GenomicFeatures_1.0.10.tgz
Package Downloads Report	Downloads Stats