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

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

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

Fred Hutchinson Cancer Research Center