rtracklayer

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.6

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 <mflawren at fhcrc.org>

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
Imports	XML (>= 1.98-0), IRanges(>= 1.3.50), GenomicRanges(>= 0.0.9), Biostrings(>= 2.15.22), BSgenome(>= 1.15.17), Biobase
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
Suggests Me	ind1KG, MotIV, oneChannelGUI, PICS, Ringo, rMAT
Version	1.8.1
Since	Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source	rtracklayer_1.8.1.tar.gz
Windows Binary	rtracklayer_1.8.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	rtracklayer_1.8.1.tgz
Package Downloads Report	Download Stats

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