R Observatory: Metrics for SuperCellCyto version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SuperCellCyto

Bioc current

SuperCell For Cytometry Data

v1.2.0 · software · GPL-3 + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.22 · Oct 30, 2025

Current · Requires R 4.6

1.0 In 2 of 49 releases 3.23

Description

SuperCellCyto provides the ability to summarise cytometry data into supercells by merging together cells that are similar in their marker expressions using the SuperCell package.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

13 3 exported

Complexity

1.4 avg / 3 max

Call network

13 nodes / 14 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

3,069

Files

44

Compiled share

0%

Has compiled src

No

Language breakdown

R 810 (26.4%)Tests 465 (15.2%)Docs 353 (11.5%)Vignettes 1,441 (47%)

API

Exported functions

3

Internal functions

10

Recent export changes

v3.22+3 recomputeSupercells, runSuperCellCyto, simCytoData

Testing & CI

Has tests

Yes

Test-to-code ratio

0.57

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

–

System requirements

–

C++ standard

–

License

GPL-3 + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

2

First release

2025-10-29

Latest release

2026-04-28

Avg cadence

181 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

READMEYes · 235 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideYes

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › CellBiology

Software › Technology › FlowCytometry

Software

Software › Technology › SingleCell

People

Givanna Putri author maintainer
Thomas Ashhurst author
George Howitt author
Felix Marsh-Wakefield author
Belinda Phipson author

At a glance

Version: 1.2.0
Category: software
License: GPL-3 + file LICENSE
Requires R: ≥ 4.6
Maintainer: Givanna Putri
Entered: 3.22 · Oct 30, 2025
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Imports

SuperCell data.table MatrixBiocParallelBioc

Suggests

flowCoreBiocknitr rmarkdown usethis testthat (>= 3.0.0)BiocSingularBiocblusterBiocscaterBiocscranBiocSeuratSingleCellExperimentBiocBiocStyleBiocmagick qs2

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SuperCellCyto")

Format

Putri, G., Ashhurst, T., Howitt, G., Marsh-Wakefield, F., & Phipson, B. (2026). SuperCellCyto: SuperCell For Cytometry Data (Version 1.2.0) [Computer software]. https://bioconductor.org/packages/SuperCellCyto

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SuperCellCyto version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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