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DEGraph

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

Two-sample tests on a graph


Bioconductor version: Development (3.19)

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 "4.4") 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

Details

biocViews DecisionTree, DifferentialExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software
Version 1.55.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License GPL-3
Depends R (>= 2.10.0), R.utils
Imports graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph
System Requirements
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Suggests corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph
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Package Archives

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

Source Package DEGraph_1.55.0.tar.gz
Windows Binary
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