RegEnrich

RegEnrich is an open-source Bioconductor R package designed to identify key gene regulators by integrating differential expression analysis, data-driven gene regulatory network inference, enrichment analysis, and gene regulator ranking using gene/protein expression profiling data. Unlike many existing tools focusing on pathway/GO enrichment analysis to identify critical genes and regulators, RegEnrich emphasizes including gene/protein regulatory interactions in its analysis.
The package utilizes the GSEA method for regulator ranking and has demonstrated superior performance through benchmarking with multiple gene expression datasets from gene silencing studies. Additionally, RegEnrich has been successfully applied to 21 publicly available datasets related to in vitro interferon stimulation across different cell types.