DOI: 10.18129/B9.bioc.cogena    

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

co-expressed gene-set enrichment analysis

Bioconductor version: Development (3.15)

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>

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PDF R Script a workflow of cogena
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biocViews Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.29.0
In Bioconductor since BioC 3.1 (R-3.2) (6.5 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
Suggests knitr, rmarkdown (>= 2.1)
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