Registration and Call for Abstracts Open for Bioc2024

cogena

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

co-expressed gene-set enrichment analysis


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
System Requirements
URL https://github.com/zhilongjia/cogena
Bug Reports https://github.com/zhilongjia/cogena/issues
See More
Suggests knitr, rmarkdown (>= 2.1)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cogena_1.37.0.tar.gz
Windows Binary cogena_1.37.0.zip
macOS Binary (x86_64) cogena_1.37.0.tgz
macOS Binary (arm64) cogena_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cogena
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cogena
Bioc Package Browser https://code.bioconductor.org/browse/cogena/
Package Short Url https://bioconductor.org/packages/cogena/
Package Downloads Report Download Stats