cageminer
Bioc currentCandidate Gene Miner
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 8 exported
Complexity
2.5 avg / 6 max
Call network
13 nodes / 11 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
2,042
Files
60
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
5
Testing & CI
Has tests
Yes
Test-to-code ratio
0.23
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 94%
- Documented parameters
- 98%
- Return-value docs
- 100%
- References docs
- 22%
Topics
People
- FabrÃcio Almeida-Silva author maintainer
- Thiago Venancio author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cageminer")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.