To discovery smaller scale, but highly correlated cellular events that may be of great biological relevance, co-expressed gene set enrichment analysis, cogena, aims to cluster gene expression profiles (coExp) for gene co-expression analysis and then implement enrichment analysis for each clusters (clEnrich) based on hyper-geometric test. The results can be visulised by heatmapCluster and heatmapPEI. Based on different gene sets used, cogena can be used as a tool for pathway analysis, GO enrichment analysis, drug repositioning and so on. See vignette for the detailed workflow.
The version of cogena at github is also availiable at Bioconductor (development version)
devtools::install_github("zhilongjia/cogena")
cogena was originally based on the clValid package.