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>

To install this package, start R and enter:

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

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

    citation("girafe")

Documentation

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

Details

biocViews Sequencing, Software
Version 1.16.0
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
Suggests Me

Package Downloads

Package Source girafe_1.16.0.tar.gz
Windows Binary girafe_1.16.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) girafe_1.16.0.tgz
Mac OS X 10.9 (Mavericks)
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