miloR
Bioc currentDifferential neighbourhood abundance testing on a graph
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
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.
None published for Bioconductor
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 →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
15,701
Files
128
Compiled share
18.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
53
Internal functions
26
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.55
testthat edition
–
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
- Help pages
- 40includes a package overview page
- Examples that run
- 100%37 run in a plain check
- Exported functions with examples
- 97%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 3%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/marionilab/milor on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| sim_discrete | list | 2 elements | No other package |
| sim_family | list | 2 elements | No other package |
| sim_nbglmm | data.frame | 250 × 8 | No other package |
| sim_trajectory | list | 2 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Mike Morgan author maintainer
- Emma Dann author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("miloR")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.