girafe

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: 2.7

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, 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		Rplots.pdf
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(>= 1.1.1), grid
Imports	methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils
Suggests	MASS, org.Mm.eg.db, RColorBrewer
System Requirements
License	Artistic-2.0
URL
Depends On Me	oneChannelGUI
Imports Me
Suggests Me
Version	1.2.0
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	girafe_1.2.0.tar.gz
Windows Binary	girafe_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	girafe_1.2.0.tgz
Package Downloads Report	Download Stats

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