├── .Rbuildignore ├── .github └── workflows │ └── r.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── Class_methods.R ├── PEI.R ├── clEnrich.R ├── clEnrich_one.R ├── coExp.R ├── cogena.R ├── cogena_class.R ├── corInCluster.R ├── dist_class.R ├── enrichment.R ├── gene2set.R ├── geneExpInCluster.R ├── geneInCluster.R ├── genecl_class.R ├── gmt2list.R ├── gmtlist2file.R ├── heatmap.3.R ├── heatmapCluster.R ├── heatmapCmap.R ├── heatmapPEI.R ├── pClusters.R ├── sota.R └── upDownGene.R ├── README.Rmd ├── README.md ├── cogena.Rproj ├── data ├── AllGeneSymbols.RData ├── Psoriasis.RData └── datalist ├── inst ├── NEWS.Rd ├── extdata │ ├── CmapDn100.gmt.xz │ ├── CmapUp100.gmt.xz │ ├── README │ ├── c2.cp.kegg.v5.0.symbols.gmt.xz │ ├── c2.cp.kegg.v7.01.symbols.gmt.xz │ └── c5.bp.v7.01.symbols.gmt.xz └── figure │ └── Cogena_workflow.png ├── man ├── AllGeneSymbols.Rd ├── DEexprs.Rd ├── PEI.Rd ├── Psoriasis.Rd ├── clEnrich.Rd ├── clEnrich_one.Rd ├── clusterMethods.Rd ├── coExp.Rd ├── cogena_class.Rd ├── 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