GSNCASCR: An R Package to Identify Differentially Co-Expressed Curated Gene Sets with Single-Cell RNA-Seq Data.

ABSTRACT: (1) Differential co-expression analysis between two phenotypes with a known gene set helps to uncover gene regulation alterations. (2) GSNCASCR uses CSCORE to estimate the gene pair correlations for network reconstruction and GSNCA to quantify the structure changes of co-expression networks of the predefined gene sets. It also ranks genes based on their "importance" in the weighted network. The method is implemented with free R software (version 0.1.0, available on GitHub), allowing users to analyze their data with the help of demo vignettes included in the package. (3) With analysis of both simulated and real datasets, we demonstrate that the statistical tests performed with GSNCASCR are able to identify differentially co-expressed gene sets with higher precision than tests with Gene Set

SUBMITTER: Gao S 

PROVIDER: S-EPMC12112291 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature