DEGraph

Two-sample tests on a graph

Bioconductor version: Release (2.7)

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

To install this package, start R and enter:

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

Documentation

PDF

R Script

DEGraph: differential expression testing for gene networks

Reference Manual

Details

biocViews	Microarray, Bioinformatics, DifferentialExpression, GraphsAndNetworks
Depends	R, R.utils
Imports	graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov
Suggests	corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz
System Requirements
License	GPL-3
URL
Depends On Me
Imports Me
Suggests Me
Version	1.0.0

Package Downloads

Package Source	DEGraph_1.0.0.tar.gz
Windows Binary	DEGraph_1.0.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	DEGraph_1.0.0.tgz
Package Downloads Report	Download Stats