GSNA

CRANGSNAMaRDI QIDQ5975775FDOQ5975775

Gene Set Networking Analysis Package

Jonathan M. Urbach

Last update: 14 February 2024

Copyright license: GNU General Public License

Software version identifier: 0.1.4.1

Description

Create networks of gene sets, infer clusters of functionally-related gene sets based on similarity statistics, and visualize 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>.

Cites work

• Functional impairment of HIV-specific CD8+ T cells precedes aborted spontaneous control of viremia
• Cytolytic CD8 + T cells infiltrate germinal centers to limit ongoing HIV replication in spontaneous controller lymph nodes

This page was built for software: GSNA