To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cogena")

In most cases, you don't need to download the package archive at all.

cogena

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see cogena.

co-expressed gene-set enrichment analysis

Bioconductor version: 3.1

Description: Gene set enrichment analysis is a valuable tool for the study of molecular mechanisms that underpin complex biological traits. As the method is conventionally used on entire omic datasets, such as transcriptomes, it may be dominated by pathways and processes that are substantially represented in a dataset, however the approach may overlook smaller scale, but highly correlated cellular events that may be of great biological relevance. In order to detect these discrete molecular triggers, we developed a tool, co-expressed gene-set enrichment analysis (cogena), for clustering differentially expressed genes and identification of highly correlated molecular expression clusters. Cogena offers the user a range of clustering methods, including hierarchical clustering, model based clustering and self-organised mapping, based on different distance metrics like correlation and mutual information. After obtaining and visualising clusters, cogena performs gene set enrichment. These gene sets can be sourced from the Molecular Signatures Database (MSigDB) or user-defined gene sets. By performing gene set enrichment across expression clusters, we find considerable enhancement in the resolution of molecular signatures in omic data at the cluster level compared to the whole.

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cogena")

Documentation

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

browseVignettes("cogena")

 

PDF cogena-vignette.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DataImport, DataRepresentation, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License LGPL-3
Depends R (>= 3.2), cluster, ggplot2, gplots, amap
Imports methods, class, foreach, parallel, doParallel, fastcluster, corrplot, reshape2, devtools
LinkingTo
Suggests Biobase, annotate, kohonen, mclust, biwt, knitr
SystemRequirements
Enhances
URL https://github.com/zhilongjia/cogena
BugReports https://github.com/zhilongjia/cogena/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source cogena_1.0.0.tar.gz
Windows Binary cogena_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) cogena_1.0.0.tgz
Mac OS X 10.9 (Mavericks) cogena_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/cogena/tree/release-3.1
Package Short Url http://bioconductor.org/packages/cogena/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center