rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.8

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, and WIG built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Author: Michael Lawrence, Vince Carey, Robert Gentleman

Maintainer: Michael Lawrence <michafla at gene.com>

To install this package, start R and enter:

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

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

    citation("rtracklayer")

Documentation

PDF R Script rtracklayer
PDF   Reference Manual

Details

biocViews Annotation, Visualization, DataImport
Depends R (>= 2.7.0), methods, RCurl (>= 1.4-2)
Imports XML (>= 1.98-0), IRanges(>= 1.9.26), GenomicRanges(>= 1.1.34), Biostrings(>= 2.15.22), BSgenome(>= 1.15.17)
Suggests humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19
System Requirements
License Artistic-2.0
URL
Depends On Me EatonEtAlChIPseq, GGtools
Imports Me ChromHeatMap, geneLenDataBase, GenomicFeatures, GGtools, R453Plus1Toolbox
Suggests Me GenomicFeatures, GGtools, ind1KG, mosaics, MotIV, oneChannelGUI, PICS, R453Plus1Toolbox, Ringo, rMAT
Version 1.12.5
Since Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source rtracklayer_1.12.5.tar.gz
Windows Binary rtracklayer_1.12.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary rtracklayer_1.12.5.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center