- Home
- Bioconductor 2.10
- Software Packages
- DEGraph
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEGraph")
In most cases, you don't need to download the package archive at all.
DEGraph
|
This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see DEGraph.
Two-sample tests on a graph
Bioconductor version: 2.10
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEGraph")
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 | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, DifferentialExpression, GraphsAndNetworks, Microarray, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (5.5 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 | graphite |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DEGraph_1.8.0.tar.gz |
| Windows Binary | DEGraph_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DEGraph/tree/release-2.10 |
| Package Short Url | http://bioconductor.org/packages/DEGraph/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
