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.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
121 6 exported
Complexity
4.6 avg / 48 max
Call network
121 nodes / 144 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
6,987
Files
92
Compiled share
2.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
8
Internal functions
105
Testing & CI
Has tests
Yes
Test-to-code ratio
0.53
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
20%
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
2026-04-28
Avg cadence
181 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
- Examples that run
- 90%
- Documented parameters
- 90%
- Return-value docs
- 100%
- References docs
- 8%
Topics
People
- Constantin Ahlmann-Eltze author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("lemur")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.
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.