lemur
Bioc currentLatent Embedding Multivariate Regression
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
126 6 exported
Complexity
4.5 avg / 48 max
Call network
126 nodes / 154 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
7,424
Files
80
Compiled share
2.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
8
Internal functions
110
Testing
Has tests
Yes
Test-to-code ratio
0.55
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
15.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-12-06
Latest release
2026-07-29
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 26 (15 internal)
- Examples that run
- 90%9 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 90%
- Return-value docs
- 100%
- Help pages citing references
- 8%
- Introduction.html HTML
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/const-ae/lemur on 2026-10-21.
Datasets
Topics
People
- Constantin Ahlmann-Eltze author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("lemur")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2023.03.06.531268.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.