DEGraph
Two-sample tests on a graph
Bioconductor version: Release (3.20)
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("DEGraph")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| DEGraph: differential expression testing for gene networks | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DecisionTree, DifferentialExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software |
| Version | 1.58.0 |
| 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 |
See More
| 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_1.58.0.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 |