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# cogena [![releaseVersion](]( [![develVersion](]( [![Bioc](]( [![Build](]( [![download](]( ## Introduction 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) ## The workflow of cogena ![cogena_workflow](inst/figure/Cogena_workflow.png) ## Installation devtools::install_github("zhilongjia/cogena") ## Help [cogena in Biostars]( ## Citation [Jia, Zhilong, et al. "Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery." BMC Genomics 17.1 (2016): 1.]( ## Acknowledgement cogena was originally based on the [clValid]( package.