cogena

DOI: 10.18129/B9.bioc.cogena    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: 3.12

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 "4.0") 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	a workflow of cogena
HTML	R Script	cogena, a workflow for gene set enrichment analysis of co-expressed genes
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.1 (R-3.2) (6 years)
License	LGPL-3
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
LinkingTo
Suggests	knitr, rmarkdown (>= 2.1)
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_1.24.0.tar.gz
Windows Binary	cogena_1.24.0.zip
macOS 10.13 (High Sierra)	cogena_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cogena
Source Repository (Developer Access)	git clone [email protected]:packages/cogena
Package Short Url	https://bioconductor.org/packages/cogena/
Package Downloads Report	Download Stats