DEGraph: Two-sample tests on a graph

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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
Date of publication
None
Maintainer
Laurent Jacob <laurent.jacob@gmail.com>
License
GPL-3
Version
1.26.0

View on Bioconductor

Man pages

annLoi2008
Annotation data used in the DEGraph package vignette
AN.test
Performs the Adaptive Neyman test of Fan and Lin (1998)
BS.test
Performs the test of Bai and Saranadasa (1996)
classLoi2008
Tamoxifen treatment resistance status data used in the...
exprLoi2008
Gene expression data used in the DEGraph package vignette
getConnectedComponentList
Given a graph, returns a list of its connected components...
getKEGGPathways
Builds a graph for each of the KEGG pathways
getSignedGraph
Given a graph, builds a signed version of the adjacency...
graph.T2.test
Performs the Hotelling T2 test in Fourier space
grListKEGG
KEGG networks used in the DEGraph package vignette
hyper.test
Performs an hypergeometric test of enrichment of a set of...
laplacianFromA
Calculates the Laplacian associated to an adjacency matrix
plotValuedGraph
Plots a graph with nodes colored according to a quantitative...
randomWAMGraph
Generates a random graph
testOneConnectedComponent
Applies a series of two-sample tests to a connected graph...
testOneGraph
Applies a serie of two-sample tests to each connected...
twoSampleFromGraph
Given a basis (typically the eigenvectors of a graph...
writeAdjacencyMatrix2KGML
Writes an adjacency matrix into an XML file

Files in this package

DEGraph/.BBSoptions
DEGraph/DESCRIPTION
DEGraph/NAMESPACE
DEGraph/R
DEGraph/R/AN.test.R
DEGraph/R/BS.test.R
DEGraph/R/getConnectedComponentList.R
DEGraph/R/getKEGGPathways.R
DEGraph/R/getSignedGraph.R
DEGraph/R/graph.T2.test.R
DEGraph/R/hyper.test.R
DEGraph/R/laplacianFromA.R
DEGraph/R/plotValuedGraph.R
DEGraph/R/randomWAMGraph.R
DEGraph/R/testOneConnectedComponent.R
DEGraph/R/testOneGraph.R
DEGraph/R/twoSampleFromGraph.R
DEGraph/R/writeAdjacencyMatrix2KGML.R
DEGraph/build
DEGraph/build/vignette.rds
DEGraph/data
DEGraph/data/Loi2008_DEGraphVignette.RData
DEGraph/demo
DEGraph/demo/00Index
DEGraph/demo/Loi2008.R
DEGraph/demo/toy.R
DEGraph/incl
DEGraph/incl/getKEGGPathways.Rex
DEGraph/incl/getSignedGraph.Rex
DEGraph/incl/graph.T2.test.Rex
DEGraph/incl/randomWAMGraph.Rex
DEGraph/incl/testOneGraph.Rex
DEGraph/incl/tests.Rex
DEGraph/inst
DEGraph/inst/CITATION
DEGraph/inst/COPYING
DEGraph/inst/NEWS
DEGraph/inst/demoScripts
DEGraph/inst/demoScripts/001.setup.R
DEGraph/inst/demoScripts/loadLoi08.R
DEGraph/inst/doc
DEGraph/inst/doc/DEGraph.R
DEGraph/inst/doc/DEGraph.Rnw
DEGraph/inst/doc/DEGraph.pdf
DEGraph/inst/downloadScripts
DEGraph/inst/downloadScripts/downloadKeggXmlFiles.R
DEGraph/inst/downloadScripts/downloadLoi08Data.R
DEGraph/inst/system
DEGraph/inst/system/generateManPages.R
DEGraph/inst/system/installPackages.R
DEGraph/man
DEGraph/man/AN.test.Rd
DEGraph/man/BS.test.Rd
DEGraph/man/annLoi2008.Rd
DEGraph/man/classLoi2008.Rd
DEGraph/man/exprLoi2008.Rd
DEGraph/man/getConnectedComponentList.Rd
DEGraph/man/getKEGGPathways.Rd
DEGraph/man/getSignedGraph.Rd
DEGraph/man/grListKEGG.Rd
DEGraph/man/graph.T2.test.Rd
DEGraph/man/hyper.test.Rd
DEGraph/man/laplacianFromA.Rd
DEGraph/man/plotValuedGraph.Rd
DEGraph/man/randomWAMGraph.Rd
DEGraph/man/testOneConnectedComponent.Rd
DEGraph/man/testOneGraph.Rd
DEGraph/man/twoSampleFromGraph.Rd
DEGraph/man/writeAdjacencyMatrix2KGML.Rd
DEGraph/vignettes
DEGraph/vignettes/DEGraph.Rnw
DEGraph/vignettes/bibli.bib