cogena
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see cogena.
co-expressed gene-set enrichment analysis
Bioconductor version: 3.17
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("cogena")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| cogena, a workflow for gene set enrichment analysis of co-expressed genes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.34.0 |
| 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_1.34.0.tar.gz |
| Windows Binary | cogena_1.34.0.zip (64-bit only) |
| macOS Binary (x86_64) | cogena_1.34.0.tgz |
| macOS Binary (arm64) | cogena_1.34.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |