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

girafe

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: 2.13

The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.

Author: Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber

Maintainer: J. Toedling <j.toedling at imb-mainz.de>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("girafe")

 

PDF	R Script	Genome intervals and read alignments for functional exploration
PDF		Reference Manual
Text		NEWS

Details

biocViews	HighThroughputSequencing, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 2.6 (R-2.11)
License	Artistic-2.0
Depends	R (>= 2.10.0), methods, IRanges(>= 1.3.53), Rsamtools, ShortRead(>= 1.3.21), intervals (>= 0.13.1), genomeIntervals(>= 1.7.3), grid
Imports	methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges
Suggests	MASS, org.Mm.eg.db, RColorBrewer
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	girafe_1.14.0.tar.gz
Windows Binary	girafe_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	girafe_1.14.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats