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

DEGraph

Two-sample tests on a graph

Bioconductor version: 2.13

DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.

Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

Maintainer: Laurent Jacob <laurent.jacob at gmail.com>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DEGraph")

 

PDF	R Script	DEGraph: differential expression testing for gene networks
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GraphsAndNetworks, Microarray, NetworkAnalysis, NetworkEnrichment, Software
Version	1.14.0
In Bioconductor since	BioC 2.7 (R-2.12)
License	GPL-3
Depends	R (>= 2.10.0), R.utils
Imports	graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph
Suggests	corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph
System Requirements
URL
Depends On Me
Imports Me
Suggests Me	graphite

Package Archives

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

Package Source	DEGraph_1.14.0.tar.gz
Windows Binary	DEGraph_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	DEGraph_1.14.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats