DEGraph

This is the development version of DEGraph; for the stable release version, see DEGraph.

Two-sample tests on a graph

Bioconductor version: Development (3.21)

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>

Citation (from within R, enter citation("DEGraph")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DEGraph")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("DEGraph")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DecisionTree, DifferentialExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software
Version	1.59.0
In Bioconductor since	BioC 2.7 (R-2.12) (14 years)
License	GPL-3
Depends	R (>= 2.10.0), R.utils
Imports	graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph
System Requirements
URL

Suggests	corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	DEGraph_1.59.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/DEGraph
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEGraph
Bioc Package Browser	https://code.bioconductor.org/browse/DEGraph/
Package Short Url	https://bioconductor.org/packages/DEGraph/
Package Downloads Report	Download Stats