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|
|Bioconductor views||DecisionTree DifferentialExpression GraphAndNetwork Microarray Network NetworkEnrichment|
|Date of publication||None|
|Maintainer||Laurent Jacob <firstname.lastname@example.org>|
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
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