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Gene Set Analysis Exploiting Pathway Topology

Bioconductor version: Release (3.1)

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 at>, Gabriele Sales <gabriele.sales at>, Chiara Romualdi <chiara.romualdi at>

Maintainer: Paolo Martini <paolo.cavei at>

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PDF R Script clipper
PDF   Reference Manual


biocViews GeneExpression, GraphAndNetwork, KEGG, Pathways, Software
Version 1.8.1
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
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
Depends On Me
Imports Me ToPASeq
Suggests Me graphite
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