CytoPipeline
Bioc currentAutomation and visualization of flow cytometry data analysis pipelines
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
79 65 exported
Complexity
8.1 avg / 54 max
Call network
79 nodes / 95 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
14,979
Files
107
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
65
Internal functions
14
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.97
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-07-04
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
- 40 (1 internal)includes a package overview page
- Examples that run
- 100%38 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/uclouvain-cbio/cytopipeline on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-08-11 · The repository has a site deploy workflow
pkgdown site last built 2026-08-11
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ChannelMarkerUsed | data.frame | 7 × 3 | No other package |
| OMIP021Samples | – | – | – |
| OMIP021_TransList | – | – | – |
| OMIP021_TransList2 | – | – | – |
| OMIP021_TransList3 | – | – | – |
Topics
Depended on by (2)
Bioconductor (2)
People
- Philippe Hauchamps author maintainer
- Laurent Gatto author
- Dan Lin contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("CytoPipeline")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-024-05691-z.
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.