topologyGSA: 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) <doi:10.1186/1752-0509-4-121>.

Version:	1.5.0
Imports:	graph, gRbase (≥ 2.0), qpgraph, fields, methods, igraph
Suggests:	Rgraphviz
Published:	2023-09-25
DOI:	10.32614/CRAN.package.topologyGSA
Author:	Sofia Massa, Gabriele Sales
Maintainer:	Gabriele Sales <gabriele.sales at unipd.it>
License:	GPL-3
NeedsCompilation:	no
In views:	Omics
CRAN checks:	topologyGSA results

Documentation:

Reference manual:

topologyGSA.html , topologyGSA.pdf

Downloads:

Package source:	topologyGSA_1.5.0.tar.gz
Windows binaries:	r-devel: topologyGSA_1.5.0.zip, r-release: topologyGSA_1.5.0.zip, r-oldrel: topologyGSA_1.5.0.zip
macOS binaries:	r-release (arm64): topologyGSA_1.5.0.tgz, r-oldrel (arm64): topologyGSA_1.5.0.tgz, r-release (x86_64): not available, r-oldrel (x86_64): topologyGSA_1.5.0.tgz
Old sources:	topologyGSA archive

Reverse dependencies:

Reverse suggests:

graphite

Linking:

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