To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cogena")

In most cases, you don't need to download the package archive at all.

cogena

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: 3.2

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 gmail.com>

Citation (from within R, enter citation("cogena")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cogena")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cogena")

 

PDF cogena-vignette.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.4.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License LGPL-3
Depends R (>= 3.2), cluster, ggplot2, kohonen
Imports methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, dplyr, devtools
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL https://github.com/zhilongjia/cogena
BugReports https://github.com/zhilongjia/cogena/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source cogena_1.4.0.tar.gz
Windows Binary cogena_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) cogena_1.4.0.tgz
Mac OS X 10.9 (Mavericks) cogena_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/cogena/tree/release-3.2
Package Short Url http://bioconductor.org/packages/cogena/
Package Downloads Report Download Stats

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