cogena
This is the released version of cogena; for the devel version, see cogena.
All Bioconductor versions of cogena
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
co-expressed gene-set enrichment analysis
Bioconductor version: 3.23 · Package version: 1.46.0
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"):
Zhilong Jia, Michael Barnes. cogena: co-expressed gene-set enrichment analysis. doi:10.18129/B9.bioc.cogena, R package version 1.46.0, https://bioconductor.org/packages/cogena.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.46.0 |
| License | LGPL-3 |
| URL | https://github.com/zhilongjia/cogena |
| Bug Reports | https://github.com/zhilongjia/cogena/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 594 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization |
| Package Short Url | https://bioconductor.org/packages/cogena/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cogena")| a workflow of cogena | HTML | R Script |
| cogena, a workflow for gene set enrichment analysis of co-expressed genes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | cogena_1.46.0.tar.gz |
| Windows binary (x86_64) | cogena_1.46.0.zip |
| macOS binary (arm64) | cogena_1.46.0.tgz |
| macOS binary (x86_64) | cogena_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cogena |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cogena |
| Package Downloads Report | Download Stats |