R Observatory: Metrics for scRepertoire version 2.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scRepertoire

Bioc current

A toolkit for single-cell immune receptor profiling

v2.8.0 · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.12 · Oct 28, 2020

Current · Requires R 4.6

1.0 In 12 of 49 releases 3.23

Description

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R single-cell workflows.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

177 44 exported

Complexity

4.6 avg / 28 max

Call network

177 nodes / 340 edges

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

Call graph

Open call graph →

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Lowest coverage

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

Code

Structure

Lines of code

25,459

Files

188

Compiled share

1%

Has compiled src

Yes

Language breakdown

R 9,085 (35.7%)C/C++/src 266 (1%)Tests 3,800 (14.9%)Docs 3,469 (13.6%)Vignettes 8,839 (34.7%)

API

Exported functions

44

Internal functions

118

Recent export changes

v3.23+2 clonalBin, vizCirclize

v3.22+2 annotateInvariant, percentGeneUsage

Testing & CI

Has tests

Yes

Test-to-code ratio

0.42

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

33.3%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

12

First release

2021-03-28

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

42

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 328 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 89%
Documented parameters: 100%
Return-value docs: 97%
References docs: 0%

Topics

Software

Software › ResearchField › Immunology › ImmunoOncology

Software › Technology › SingleCell

Software › StatisticalMethod › Classification

Software › WorkflowStep › Annotation

Software › Technology › Sequencing

Depended on by (5)

Bioconductor (5)

dandelionR Ibex immApex immLynx immGLIPH

People

Nick Borcherding author maintainer
Justin Reimertz contributor
Ksenia Safina author
Qile Yang author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scRepertoire")

Format

Borcherding, N., Reimertz, J., Safina, K., & Yang, Q. (2026). scRepertoire: A toolkit for single-cell immune receptor profiling (Version 2.8.0) [Computer software]. https://bioconductor.org/packages/scRepertoire

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 scRepertoire version 2.8.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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