R Observatory: Metrics for SpaNorm version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SpaNorm

Bioc current

Spatially-aware normalisation for spatial transcriptomics data

v1.6.0 · software · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

62 3 exported

Complexity

4.8 avg / 29 max

Call network

62 nodes / 88 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

3,920

Files

52

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,307 (58.9%)Tests 725 (18.5%)Docs 533 (13.6%)Vignettes 355 (9.1%)

API

Exported functions

8

Internal functions

58

Recent export changes

v3.23+4 SpaNormPCA, SpaNormSVG, plotCovariate +1 more

v3.20+4 SpaNorm, fastSizeFactors, filterGenes +1 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.31

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

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4

System requirements

–

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

4

First release

2024-10-29

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

–

Dep drift

2

LOC over versions

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

Documentation

READMEYes · 271 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 9%

Topics

Software

Software › AssayDomain › GeneExpression

Software › ResearchField › Transcriptomics

Software › Technology › Spatial

Software › ResearchField › CellBiology

People

Dharmesh D. Bhuva author maintainer
Ahmed Mohamed author
Agus Salim author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SpaNorm")

Format

Bhuva, D. D., Mohamed, A., & Salim, A. (2026). SpaNorm: Spatially-aware normalisation for spatial transcriptomics data (Version 1.6.0) [Computer software]. https://bioconductor.org/packages/SpaNorm

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 SpaNorm version 1.6.0 [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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