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topologyGSA  

Gene Set Analysis Exploiting Pathway Topology
View on CRAN: Click here


Download and install topologyGSA package within the R console
Install from CRAN:
install.packages("topologyGSA")

Install from Github:
library("remotes")
install_github("cran/topologyGSA")

Install by package version:
library("remotes")
install_version("topologyGSA", "1.5.0")



Attach the package and use:
library("topologyGSA")
Maintained by
Gabriele Sales
[Scholar Profile | Author Map]
First Published: 2011-06-24
Latest Update: 2023-09-25
Description:
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>.
How to cite:
Gabriele Sales (2011). topologyGSA: Gene Set Analysis Exploiting Pathway Topology. R package version 1.5.0, https://cran.r-project.org/web/packages/topologyGSA. Accessed 09 May. 2025.
Previous versions and publish date:
1.0.2 (2011-11-10 14:37), 1.0.3 (2011-12-22 12:22), 1.0 (2011-06-24 18:58), 1.1.0 (2012-07-18 16:10), 1.2.0 (2013-03-01 15:06), 1.2.1 (2013-06-26 09:28), 1.4.0 (2013-10-23 18:34), 1.4.1 (2013-11-19 19:21), 1.4.2 (2013-12-12 16:48), 1.4.3 (2014-03-26 17:46), 1.4.4 (2014-08-02 18:27), 1.4.5 (2015-07-09 18:13), 1.4.6 (2016-09-22 16:51), 1.4.7 (2021-07-07 14:20)
Other packages that cited topologyGSA R package
View topologyGSA citation profile
Other R packages that topologyGSA depends, imports, suggests or enhances
Complete documentation for topologyGSA
Functions, R codes and Examples using the topologyGSA R package
Some associated functions: clique.mean.test . clique.var.test . dag_bcell . pathway.mean.test . pathway.var.test . print . render.significant.cliques . y1 . y2 . 
Some associated R codes: cliques.R . cov.R . graph.R . hote.R . multt.R . params.R . pathway.R . print.R . render.R .  Full topologyGSA package functions and examples
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