cyanoFilter
Bioc currentPhytoplankton Population Identification using Cell Pigmentation and/or Complexity
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 30 exported
Complexity
2.7 avg / 8 max
Call network
30 nodes / 18 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
4,899
Files
74
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
0
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
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 46includes a package overview page
- Examples that run
- 100%37 run in a plain check
- Exported functions with examples
- 93%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/fomotis/cyanofilter on 2026-10-22.
Datasets
Topics
People
- Oluwafemi Olusoji maintainer author
- Delaender Frederik contributor
- Aerts Marc contributor
- Neyens Thomas contributor
- Spaak jurg author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cyanoFilter")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.