pyLemur

The Python implementation of the LEMUR method to analyze multi-condition single-cell data. For the more complete version in R, see github.com/const-ae/lemur. To learn more check-out the function documentation and the tutorial at pylemur.readthedocs.io. To check-out the source code or submit an issue go to github.com/const-ae/pyLemur

Citation

Ahlmann-Eltze C, Huber W (2025). “Analysis of multi-condition single-cell data with latent embedding multivariate regression.” Nature Genetics (2025). doi:10.1038/s41588-024-01996-0.

Getting started

Installation

You need to have Python 3.10 or newer installed on your system. There are several alternative options to install pyLemur:

Install the latest release of pyLemur from PyPI:

pip install pyLemur

Alternatively, install the latest development version directly from Github:

pip install git+https://github.com/const-ae/pyLemur.git@main

Documentation

For more information on the functions see the API docs and the tutorial.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Building

Install the package in editable mode:

pip install ".[dev,doc,test]"

Build the documentation locally

cd docs
make html
open _build/html/index.html

Run the unit tests

pytest

Run pre-commit hooks manually

pre-commit run --all-files

or individually

ruff check