DESCRIPTION

Package: cogena
Version: 1.21.2
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