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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DEGraph")
In most cases, you don't need to download the package archive at all.
DEGraph
Two-sample tests on a graph
Bioconductor version: 3.0
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:
source("http://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")
| R Script | DEGraph: differential expression testing for gene networks | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DecisionTree, DifferentialExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| 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, ToPASeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DEGraph_1.18.0.tar.gz |
| Windows Binary | DEGraph_1.18.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DEGraph_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | DEGraph_1.18.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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