Package: cogena
Version: 1.47.0
Title: co-expressed gene-set enrichment analysis
Authors@R: c(person("Zhilong", "Jia", role =c("aut", "cre"), 
    email="zhilongjia@gmail.com"), 
    person("Michael", "Barnes", role = "aut", email="m.r.barnes@qmul.ac.uk"))
Description: 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.
biocViews: Clustering, GeneSetEnrichment, GeneExpression,
        Visualization, Pathways, KEGG, GO, Microarray, Sequencing,
        SystemsBiology, DataRepresentation, DataImport
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)
Collate: dist_class.R genecl_class.R cogena_class.R Class_methods.R
        cogena.R upDownGene.R PEI.R sota.R pClusters.R coExp.R
        clEnrich.R clEnrich_one.R enrichment.R gene2set.R
        geneInCluster.R geneExpInCluster.R corInCluster.R gmt2list.R
        gmtlist2file.R heatmap.3.R heatmapCluster.R heatmapPEI.R
        heatmapCmap.R
License: LGPL-3
LazyData: true
Encoding: UTF-8
URL: https://github.com/zhilongjia/cogena
NeedsCompilation: no
BugReports: https://github.com/zhilongjia/cogena/issues
VignetteBuilder: knitr
RoxygenNote: 7.0.2
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev git make libharfbuzz-dev libgit2-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:41:05 UTC
RemoteUrl: https://github.com/bioc/cogena
RemoteRef: HEAD
RemoteSha: 4a6fc62eb0817d06b7176caafdf7408de7964c3e
Packaged: 2026-07-04 22:58:19 UTC; root
Author: Zhilong Jia [aut, cre],
  Michael Barnes [aut]
Maintainer: Zhilong Jia <zhilongjia@gmail.com>