DEGraph: Two-sample tests on a graph

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.

AuthorLaurent Jacob, Pierre Neuvial and Sandrine Dudoit
Date of publicationNone
MaintainerLaurent Jacob <laurent.jacob@gmail.com>
LicenseGPL-3
Version1.26.0

View on Bioconductor

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

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