GSBenchMark
Bioc currentGene Set Benchmark
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
2,374
Files
42
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
–
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.13.1
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-12-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 17includes a package overview page
- Examples that run
- 100%16 run in a plain check
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 100%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GSBenchMark.Dataset.names | vector | 11 elements | No other package |
| diracpathways | list | 249 elements | No other package |
| exprsdata | matrix | 22,283 × 61 | No other package |
| logexprsdata | matrix | 22,283 × 61 | No other package |
| phenotypes | factor | 61 elements | No other package |
| phenotypesLevels | vector | 2 elements | No other package |
Topics
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("GSBenchMark")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.