R Observatory: Metrics for spoon version 1.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spoon

Bioc current

Address the Mean-variance Relationship in Spatial Transcriptomics Data

v1.8.0 · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.19 · May 1, 2024

Current · Requires R 4.6

1.0 In 5 of 49 releases 3.23

Description

This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

4 2 exported

Complexity

4.3 avg / 9 max

Call network

4 nodes / 2 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

858

Files

22

Compiled share

0%

Has compiled src

No

Language breakdown

R 467 (54.4%)Tests 23 (2.7%)Docs 194 (22.6%)Vignettes 174 (20.3%)

API

Exported functions

2

Internal functions

2

Recent export changes

v3.19+2 generate_weights, weighted_nnSVG

Testing & CI

Has tests

Yes

Test-to-code ratio

0.05

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

4.4

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

5

First release

2024-04-30

Latest release

2026-04-28

Avg cadence

182 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 · 1,874 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 0%

Topics

Software › Technology › Spatial

Software › Technology › SingleCell

Software › ResearchField › Transcriptomics

Software › AssayDomain › GeneExpression

Software › WorkflowStep › Preprocessing

People

Kinnary Shah author maintainer
Boyi Guo author
Stephanie C. Hicks author

At a glance

Version: 1.8.0
Category: software
License: MIT + file LICENSE
Requires R: ≥ 4.6
Maintainer: Kinnary Shah
Entered: 3.19 · May 1, 2024
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.4)

Imports

SpatialExperimentBiocBRISCnnSVGBiocBiocParallelBiocMatrixmethodsSummarizedExperimentBiocstatsutilsscuttleBioc

Suggests

testthatSTexampleDataBiocknitr rmarkdownBiocStyleBioc

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spoon")

Format

Shah, K., Guo, B., & Hicks, S. C. (2026). spoon: Address the Mean-variance Relationship in Spatial Transcriptomics Data (Version 1.8.0) [Computer software]. https://bioconductor.org/packages/spoon

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 spoon version 1.8.0 [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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