girafe

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: 2.8

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 <joern.toedling at curie.fr>

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

Details

biocViews Sequencing, HighThroughputSequencing
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
License Artistic-2.0
URL
Depends On Me oneChannelGUI
Imports Me
Suggests Me
Version 1.4.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source girafe_1.4.0.tar.gz
Windows Binary girafe_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary girafe_1.4.0.tgz
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