cogena

Package: cogena
Version: 1.6.2
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 (>= 3.2), cluster, ggplot2, kohonen
Imports: methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, dplyr, devtools
Suggests: knitr, rmarkdown
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: 5.0.1
Packaged: 2016-05-16 05:25:45 UTC; biocbuild
Author: Zhilong Jia [aut, cre],
Michael Barnes [aut]
Maintainer: Zhilong Jia <zhilongjia@gmail.com>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cogena' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'cogena'
** help
*** installing help indices
  converting help for package 'cogena'
    finding HTML links ... done
    AllGeneSymbols                          html  
    DEexprs                                 html  
    PEI                                     html  
    Psoriasis                               html  
    clEnrich                                html  
    clEnrich_one                            html  
    clusterMethods                          html  
    coExp                                   html  
    cogena_class                            html  
    cogena_package                          html  
    corInCluster                            html  
    enrichment                              html  
    gene2set                                html  
    geneExpInCluster                        html  
    geneInCluster                           html  
    genecl_class                            html  
    geneclusters                            html  
    gmt2list                                html  
    gmtlist2file                            html  
    heatmap.3                               html  
    heatmapCluster                          html  
    heatmapCmap                             html  
    heatmapPEI                              html  
    mat                                     html  
    nClusters                               html  
    pClusters                               html  
    sampleLabel                             html  
    show                                    html  
    sota                                    html  
    summary                                 html  
    upDownGene                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cogena)
Making 'packages.html' ... done