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 3.4 of Bioconductor; for the stable, up-to-date release version, see cogena.
co-expressed gene-set enrichment analysis
Bioconductor version: 3.4
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 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")
| R Script | Vignette Title | |
| HTML | R Script | Vignette Title |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | LGPL-3 |
| Depends | R (>= 3.2), cluster, ggplot2, kohonen |
| Imports | methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, dplyr, devtools |
| LinkingTo | |
| Suggests | knitr, rmarkdown |
| 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_1.8.0.tar.gz |
| Windows Binary | cogena_1.8.0.zip |
| Mac OS X 10.9 (Mavericks) | cogena_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/cogena/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/cogena/ |
| Package Downloads Report | Download Stats |
Documentation »
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