Gene Set Analysis Exploiting Pathway Topology

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) .


Reference manual

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install.packages("topologyGSA")

1.5.0 by Gabriele Sales, 3 years ago


Browse source code at https://github.com/cran/topologyGSA


Authors: Sofia Massa , Gabriele Sales


Documentation:   PDF Manual  


GPL-3 license


Imports graph, gRbase, qpgraph, fields, methods, igraph

Suggests Rgraphviz


See at CRAN