R Observatory: Metrics for miloR version 2.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

miloR

Bioc current

Differential neighbourhood abundance testing on a graph

v2.8.1 · software · GPL-3 + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.13 · May 20, 2021

Current · Requires R 4.6

1.0 In 11 of 49 releases 3.23

Description

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

129 35 exported

Complexity

8 avg / 78 max

Call network

129 nodes / 84 edges

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

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

15,702

Files

186

Compiled share

18.9%

Has compiled src

Yes

Language breakdown

R 5,818 (37.1%)C/C++/src 2,971 (18.9%)Tests 3,183 (20.3%)Docs 2,506 (16%)Vignettes 1,224 (7.8%)

API

Exported functions

53

Internal functions

26

Recent export changes

v3.19+10 .parse_formula, .rEParse, Satterthwaite_df +7 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.55

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

94.3%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

GPL-3 + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

11

First release

2021-05-19

Latest release

2026-05-11

Avg cadence

186 days

Cold removal rate

–

Dep drift

6

LOC over versions

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

Documentation

READMEYes · 441 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 3%

Topics

Software › Technology › SingleCell

Software › WorkflowStep › MultipleComparison

Software › ResearchField › FunctionalGenomics

Software

Depended on by (1)

Bioconductor (1)

dandelionR

People

Mike Morgan author maintainer
Emma Dann author contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("miloR")

Format

Morgan, M., & Dann, E. (2026). miloR: Differential neighbourhood abundance testing on a graph (Version 2.8.1) [Computer software]. https://bioconductor.org/packages/miloR

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 miloR version 2.8.1 [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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