staRgate
Bioc currentAutomated gating pipeline for flow cytometry analysis to characterize the lineage, differentiation, and functional states of T-cells
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
An R-based automated gating pipeline for flow cytometry data designed to mimic the manual gating strategy of defining flow biomarker positive populations relative to a unimodal background population to include cells with varying intensities of marker expression. The pipeline’s main feature is a flexible density-based gating strategy capable of capturing varying scenarios based on marker expression patterns to analyze a 29-marker flow panel that characterizes T-cell lineage, differentiation, and functional states.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 5 exported
Complexity
7.7 avg / 30 max
Call network
9 nodes / 6 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
3,904
Files
52
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.51
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
4.3.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Jasme Lee author maintainer
- MSK-MIND fnd
- NIH P30CA008748 fnd
- NIH R01CA276286 fnd
- V foundation fnd
- Matthew Adamow author
- Margaret K Callahan author
- Fiona Ehrich author
- Colleen Maher author
- Katherine S Panageas author
- Xiyu Peng author
- Michael A Postow author
- Ronglai Shen author
- Phillip Wong author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("staRgate")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.