cogena
Bioc currentco-expressed gene-set enrichment analysis
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
24 9 exported
Complexity
9.5 avg / 120 max
Call network
24 nodes / 20 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,493
Files
74
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
15
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
16.7%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
LGPL-3
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-04-16
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 78%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 3%
Topics
People
- Zhilong Jia author maintainer
- Michael Barnes author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cogena")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.