To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("cogena")

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

cogena

DOI: 10.18129/B9.bioc.cogena    

This is the development version of cogena; for the stable release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: Development (3.6)

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("http://bioc.ism.ac.jp/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 R Script Vignette Title
HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.11.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
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, rmarkdown
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.

Source Package cogena_1.11.0.tar.gz
Windows Binary cogena_1.11.0.zip
Mac OS X 10.11 (El Capitan) cogena_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cogena
Package Short Url http://bioconductor.org/packages/cogena/
Package Downloads Report Download Stats

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