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Gene set analysis exploiting pathway topology

Bioconductor version: 2.14

clipper is a package for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to 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 at>, Gabriele Sales <gabriele.sales at>, Chiara Romualdi <chiara.romualdi at>

Maintainer: Paolo Martini <paolo.cavei at>

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biocViews Software
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License AGPL-3
Depends R (>= 2.15.0), Matrix, graph
Imports methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL
Suggests RUnit, BiocGenerics, RCytoscape(>= 1.6.3), graphite, ALL, hgu95av2.db, MASS, BiocStyle
System Requirements
Depends On Me
Imports Me
Suggests Me graphite

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