GSNA, Version v0.1.4.1

This is the first public release of GSNA on CRAN.

GSNA stands for Gene Set Network Analysis, and it is a set of tools for creating networks of gene sets, inferring clusters of functionally-related gene sets based on similarity statistics, and visualization of the results. This package simplifies and accelerates interpretation of pathways analysis data sets. It is designed to work in tandem with standard pathways analysis methods, such as the 'GSEA' program (Gene Set Enrichment Analysis), CERNO (Coincident Extreme Ranks in Numerical Observations, implemented in the 'tmod' package) and others. Inputs to 'GSNA' are the outputs of pathways analysis methods: a list of gene sets (or "modules"), pathways or GO-terms with associated p-values. Since pathways analysis methods may be used to analyze many different types of data including transcriptomic, epigenetic, and high-throughput screen data sets, the 'GSNA' pipeline is applicable to these data as well. The use of 'GSNA' has been described in the following papers:

• Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, et al. (2021) doi:10.1016/j.immuni.2021.08.007
• Collins DR, Hitschfel J, Urbach JM, Mylvaganam GH, Ly NL, Arshad U, et al. (2023) doi:10.1126/sciimmunol.ade5872.