clipper: Gene Set Analysis Exploiting Pathway Topology

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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.

Author
Paolo Martini <paolo.cavei@gmail.com>, Gabriele Sales <gabriele.sales@unipd.it>, Chiara Romualdi <chiara.romualdi@unipd.it>
Date of publication
None
Maintainer
Paolo Martini <paolo.cavei@gmail.com>
License
AGPL-3
Version
1.14.0

View on Bioconductor

Man pages

clipper
Dissect the pathway to find the path with the greatest...
clipperAllRoots
Dissect the pathway to find the path with the greatest...
cliqueMeanTest
Mean test for cliques.
cliqueMixedTest
Mean test for cliques.
cliquePairedTest
Paired mean test for cliques.
cliqueVarianceTest
Variance test for cliques.
deleteEdge
Remove an edge from 'graphNel' object.
easyClip
Easy clip analysis.
easyLook
Summarize clipper output.
getGraphEntryGenes
Extract all the possible entry point (genes with no entering...
getJunctionTreePaths
Extract the shortest paths along the junction tree of the...
nameCliques
Generate clique names from their own elements.
pathwayTest
Whole pathway test using qpipf.
plotInCytoscape
Plot a pathway graph in Cytoscape highlighting the relevant...
prunePaths
Summarize the paths obtained by clipper according to their...

Files in this package

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