cogena

DOI: 10.18129/B9.bioc.cogena    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cogena")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("cogena")

 

PDF	R Script	cogena Tutorial
HTML	R Script	cogena Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	LGPL-3
Depends	R (>= 3.4), 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
Links To Me
Build Report

Package Archives

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

Source Package	cogena_1.16.0.tar.gz
Windows Binary	cogena_1.16.0.zip
Mac OS X 10.11 (El Capitan)	cogena_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cogena
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cogena
Package Short Url	http://bioconductor.org/packages/cogena/
Package Downloads Report	Download Stats