cogena
co-expressed gene-set enrichment analysis
Bioconductor version: 3.23 · Package version: 1.46.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cogena")Details
| Maintainer | Zhilong Jia <zhilongjia@gmail.com> |
| Author | Zhilong Jia [aut, cre], Michael Barnes [aut] |
| License | LGPL-3 |
| URL | https://github.com/zhilongjia/cogena |
| Bug Reports | https://github.com/zhilongjia/cogena/issues |
| 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/ |
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.
Documentation
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 |