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 (3.12)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 1.23.0
In Bioconductor since BioC 3.1 (R-3.2) (5 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_1.23.0.tar.gz
Windows Binary cogena_1.23.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) cogena_1.23.0.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 https://bioconductor.org/packages/cogena/
Package Downloads Report Download Stats

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