DEGraph

DOI: 10.18129/B9.bioc.DEGraph    

Two-sample tests on a graph

Bioconductor version: Release (3.13)

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 (version "4.1") and enter:

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

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")

 

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

Details

biocViews	DecisionTree, DifferentialExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software
Version	1.44.0
In Bioconductor since	BioC 2.7 (R-2.12) (11 years)
License	GPL-3
Depends	R (>= 2.10.0), R.utils
Imports	graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph
LinkingTo
Suggests	corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	DEGraph_1.44.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/DEGraph
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEGraph
Package Short Url	https://bioconductor.org/packages/DEGraph/
Package Downloads Report	Download Stats