GSEABenchmarkeR
Bioc currentReproducible GSEA Benchmarking
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
61 19 exported
Complexity
3.6 avg / 15 max
Call network
61 nodes / 63 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
4,336
Files
33
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
42
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
186 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 8%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/waldronlab/gseabenchmarker on 2026-10-11.
GitHub Pages site
Datasets
Topics
Suggested by (2)
People
- Ludwig Geistlinger author maintainer
- Gergely Csaba author
- Marcel Ramos contributor
- Mara Santarelli contributor
- Lucas Schiffer contributor
- Levi Waldron author
- Ralf Zimmer author
Cite
Cite this package
Run in R for the authors' entry:
citation("GSEABenchmarkeR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bib/bbz158.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.