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This is the development version of cogena; for the stable release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: Development (3.20)

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

Author: Zhilong Jia [aut, cre], Michael Barnes [aut]

Maintainer: Zhilong Jia <zhilongjia at>

Citation (from within R, enter citation("cogena")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

a workflow of cogena PDF R Script
cogena, a workflow for gene set enrichment analysis of co-expressed genes HTML R Script
Reference Manual PDF


biocViews Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.39.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License LGPL-3
Depends R (>= 3.6), cluster, ggplot2, kohonen
Imports methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools
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Source Package cogena_1.39.0.tar.gz
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