pipeComp
Bioc currentpipeComp pipeline benchmarking framework
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
68 28 exported
Complexity
7 avg / 29 max
Call network
68 nodes / 62 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
5,676
Files
77
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
28
Internal functions
40
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
–
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
License flags
not SPDX, not OSI
History
Versions
12
First release
2020-10-27
Latest release
2026-05-26
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
- 36includes a package overview page
- Examples that run
- 100%27 run in a plain check
- Exported functions with examples
- 93%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 3%
- pipeComp_dea HTML
- pipeComp_scRNA HTML
- pipeComp HTML
Repository practices
Checks run against github.com/plger/pipecomp on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| clustMetricsCorr | list | 2 elements | No other package |
| ctrlgenes | list | 2 elements | No other package |
| exampleDEAresults | – | – | – |
| exampleResults | – | – | – |
| stableG | list | 2 elements | No other package |
Topics
People
- Pierre-Luc Germain maintainer author
- Mark D. Robinson author funder
- Anthony Sonrel author
Cite
Cite this package
Run in R for the authors' entry:
citation("pipeComp")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-020-02136-7.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.