R Observatory: Metrics for BayesSpace version 1.22.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BayesSpace

Bioc current

Clustering and Resolution Enhancement of Spatial Transcriptomes

v1.22.0 · 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

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

94 18 exported

Complexity

3.9 avg / 20 max

Call network

94 nodes / 75 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

6,803

Files

94

Compiled share

26.5%

Has compiled src

Yes

Language breakdown

R 2,890 (42.5%)C/C++/src 1,804 (26.5%)Tests 234 (3.4%)Docs 1,585 (23.3%)Vignettes 290 (4.3%)

API

Exported functions

18

Internal functions

45

Recent export changes

v3.20+5 adjustClusterLabels, coreTune, counts2h5 +2 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.08

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

6.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

1

C++ standard

C++17

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

12

First release

2020-10-27

Latest release

2026-04-28

Avg cadence

177 days

Cold removal rate

–

Dep drift

11

LOC over versions

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

Documentation

READMEYes · 325 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 94%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › StatisticalMethod › Clustering

Software › ResearchField › Transcriptomics

Software › AssayDomain › GeneExpression

Software › Technology › SingleCell

Software › ResearchField › Immunology › ImmunoOncology

Software › Infrastructure › DataImport

Depended on by (2)

Bioconductor (2)

RegionalST OSTA

People

Senbai Kang author maintainer
Raphael Gottardo contributor
Xing Ren contributor
Matt Stone author
Edward Zhao author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BayesSpace")

Format

Kang, S., Gottardo, R., Ren, X., Stone, M., & Zhao, E. (2026). BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes (Version 1.22.0) [Computer software]. https://bioconductor.org/packages/BayesSpace

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 BayesSpace version 1.22.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

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.

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