openCyto
Bioc currentHierarchical Gating Pipeline for flow cytometry data
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
174 44 exported
Complexity
4.8 avg / 39 max
Call network
174 nodes / 134 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
13,134
Files
164
Compiled share
6%
Has compiled src
Yes
Language breakdown
API
Exported functions
48
Internal functions
104
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.14
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
30.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
C++17
License
AGPL-3.0-only
License flags
not SPDX, not OSI
History
Versions
26
First release
2014-03-11
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
58.3%
Dep drift
14
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 71 (1 internal)includes a package overview page
- Examples that run
- 11%3 run in a plain check · 25 never run
- Exported functions with examples
- 79%
- Documented parameters
- 89%
- Return-value docs
- 54%
- Help pages citing references
- 0%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
3 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ICS | data.frame | 17 × 11 | No other package |
| ICS_080 | data.frame | 31 × 10 | No other package |
| ITN_Newell | data.frame | 19 × 10 | No other package |
| bcell | data.frame | 19 × 10 | No other package |
| tcell | data.frame | 11 × 10 | No other package |
| testGatingTemplate | data.frame | 10 × 10 | No other package |
| treg | data.frame | 18 × 10 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("openCyto")The package provides a citation file, so citation() returns the authors' own entry.
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.