cogena

DOI:10.18129/B9.bioc.cogena

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, seecogena.

co-expressed gene-set enrichment analysis

Bioconductor version: 3.16

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

Installation

To install this package, start R (version "4.2") and enter:

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

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

Documentation

查看文档的版本包age 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	1.32.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 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

Followbob 体育网址 instructions to use this package in your R session.

Source Package	cogena_1.32.0.tar.gz
Windows Binary	cogena_1.32.0.zip
macOS Binary (x86_64)	cogena_1.32.0.tgz
macOS Binary (arm64)	cogena_1.32.0.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	//www.anjoumacpherson.com/packages/cogena/
Package Downloads Report	Download Stats