R Observatory: Metrics for DenoIST version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DenoIST

Bioc current

DenoIST: Denoising Image-based Spatial Transcriptomics data

v1.0.0 · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.23 · Apr 29, 2026

Current · Requires R 4.6

1.0 In 1 of 49 releases 3.23

Description

DenoIST identifies and removes contamination in Image-based Spatial Transcriptomics data, using a transposed poisson mixture model with local neighbourhood offsets to infer genes that are likely to be due to neighbourhood contamination rather than endogenous expression.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

4 4 exported

Complexity

11.5 avg / 14 max

Call network

4 nodes / 3 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

1,306

Files

35

Compiled share

0%

Has compiled src

No

Language breakdown

R 698 (53.4%)Tests 178 (13.6%)Docs 282 (21.6%)Vignettes 148 (11.3%)

API

Exported functions

4

Internal functions

0

Recent export changes

v3.23+4 denoist, local_offset_distance_with_background, local_offset_distance_with_background_fast +1 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.26

testthat edition

–

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

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

1

First release

2026-04-28

Latest release

2026-04-28

Avg cadence

–

Cold removal rate

–

Dep drift

0

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

Documentation

READMEYes · 489 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Topics

Software

Software › WorkflowStep › Preprocessing

Software › Technology › Spatial

Software › AssayDomain › GeneExpression

Software › Technology › SingleCell

Software › ResearchField › Transcriptomics

People

Aaron Kwok author maintainer
Davis McCarthy author
Heejung Shim author

At a glance

Version: 1.0.0
Category: software
License: MIT + file LICENSE
Requires R: ≥ 4.6
Maintainer: Aaron Kwok
Entered: 3.23 · Apr 29, 2026
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.5.0)

Imports

flexmix hexbin pbapplysparseMatrixStatsBiocSpatialExperimentBiocstatsSummarizedExperimentBiocparallelMatrix dbscanmethods

Suggests

BiocStyleBiocknitr rmarkdown testthat ggplot2 patchwork

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DenoIST")

Format

Kwok, A., McCarthy, D., & Shim, H. (2026). DenoIST: DenoIST: Denoising Image-based Spatial Transcriptomics data (Version 1.0.0) [Computer software]. https://bioconductor.org/packages/DenoIST

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 DenoIST version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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