clipper: Gene Set Analysis Exploiting Pathway Topology

Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

AuthorPaolo Martini <paolo.cavei@gmail.com>, Gabriele Sales <gabriele.sales@unipd.it>, Chiara Romualdi <chiara.romualdi@unipd.it>
Date of publicationNone
MaintainerPaolo Martini <paolo.cavei@gmail.com>
LicenseAGPL-3
Version1.14.0

View on Bioconductor

Files

clipper/COPYING
clipper/DESCRIPTION
clipper/NAMESPACE
clipper/R
clipper/R/clipper.R clipper/R/clipperBackbone.R clipper/R/cliqueHandling.R clipper/R/cliqueMeanTest.R clipper/R/cliqueMixedTest.R clipper/R/cliquePairedTest.R clipper/R/cliqueVarianceTest.R clipper/R/covariance.R clipper/R/dag-graph.R clipper/R/deleteEdge.R clipper/R/easyClip.R clipper/R/easyLook.R clipper/R/getExpression.R clipper/R/getGraphEntryGenes.R clipper/R/getJunctionTreePaths.R clipper/R/graph-theory.R clipper/R/hotePaired.R clipper/R/hotelling4mean.R clipper/R/hotelling4qpipf.R clipper/R/multiTest.R clipper/R/pathwayTest.R clipper/R/permutation.R clipper/R/plotInCytoscape.R clipper/R/prunePaths.R clipper/R/removeNArows.R clipper/R/removeSelfLoops.R
clipper/build
clipper/build/vignette.rds
clipper/inst
clipper/inst/doc
clipper/inst/doc/clipper.R
clipper/inst/doc/clipper.Rnw
clipper/inst/doc/clipper.pdf
clipper/inst/unitTests
clipper/inst/unitTests/test_clipper.R
clipper/inst/unitTests/test_cliqueMeanTest.R
clipper/inst/unitTests/test_cliquePairedTest.R
clipper/inst/unitTests/test_cliqueVarianceTest.R
clipper/inst/unitTests/test_deleteEdge.R
clipper/inst/unitTests/test_getGraphEntryGenes.R
clipper/inst/unitTests/test_getJunctionTreePaths.R
clipper/inst/unitTests/test_patQ.R
clipper/inst/unitTests/test_pathQ-paired.R
clipper/inst/unitTests/test_prunePaths.R
clipper/man
clipper/man/clipper.Rd clipper/man/clipperAllRoots.Rd clipper/man/cliqueMeanTest.Rd clipper/man/cliqueMixedTest.Rd clipper/man/cliquePairedTest.Rd clipper/man/cliqueVarianceTest.Rd clipper/man/deleteEdge.Rd clipper/man/easyClip.Rd clipper/man/easyLook.Rd clipper/man/getGraphEntryGenes.Rd clipper/man/getJunctionTreePaths.Rd clipper/man/nameCliques.Rd clipper/man/pathwayTest.Rd clipper/man/plotInCytoscape.Rd clipper/man/prunePaths.Rd
clipper/tests
clipper/tests/runTests.R
clipper/vignettes
clipper/vignettes/Cytoscape.png
clipper/vignettes/clipper.Rnw

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