To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

girafe

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: Release (2.14)

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 <jtoedling at yahoo.de>

Citation (from within R, enter citation("girafe")):

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 Sequencing, Software
Version 1.16.1
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
Suggests Me

Package Archives

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

Package Source girafe_1.16.1.tar.gz
Windows Binary girafe_1.16.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) girafe_1.16.1.tgz
Mac OS X 10.9 (Mavericks) girafe_1.16.1.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

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

Fred Hutchinson Cancer Research Center