GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.7

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 <bioconductor at stat.math.ethz.ch>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("GenomicFeatures")

Documentation

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

Details

biocViews	Genetics, Infrastructure, Annotation, HighThroughputSequencing
Depends	IRanges(>= 1.7.7), GenomicRanges(>= 0.0.9)
Imports	methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), IRanges, GenomicRanges, Biostrings(>= 2.17.6), rtracklayer(>= 1.7.11), biomaRt, RCurl, utils
Suggests	rtracklayer, biomaRt, org.Mm.eg.db, GenomicFeatures.Hsapiens.UCSC.hg18, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me	GenomicFeatures.Hsapiens.UCSC.hg18, GenomicFeatures.Mmusculus.UCSC.mm9
Imports Me	geneLenDataBase, GenomicFeatures.Hsapiens.UCSC.hg18, GenomicFeatures.Mmusculus.UCSC.mm9
Suggests Me	Biostrings, chipseq, GenomicRanges, ind1KG, Rsamtools
Version	1.2.3
Since	Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source	GenomicFeatures_1.2.3.tar.gz
Windows Binary	GenomicFeatures_1.2.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicFeatures_1.2.3.tgz
Package Downloads Report	Download Stats

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