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https://github.com/const-ae/pylemur
A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
https://github.com/const-ae/pylemur
Last synced: about 2 months ago
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A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
- Host: GitHub
- URL: https://github.com/const-ae/pylemur
- Owner: const-ae
- License: mit
- Created: 2024-03-11T12:08:32.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-04-17T12:11:29.000Z (9 months ago)
- Last Synced: 2024-04-17T18:16:41.977Z (9 months ago)
- Language: Python
- Size: 3.02 MB
- Stars: 8
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# pyLemur
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/const-ae/pyLemur/test.yaml?branch=main
[link-tests]: https://github.com/const-ae/pyLemur/actions/workflows/test.yaml
[link-docs]: https://pyLemur.readthedocs.io
[badge-docs]: http://readthedocs.org/projects/pylemur/badge
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](https://github.com/const-ae/lemur). To learn more check-out the [function documentation](https://pylemur.readthedocs.io/page/api.html) and the [tutorial](https://pylemur.readthedocs.io/page/notebooks/Tutorial.html) at [pylemur.readthedocs.io](https://pylemur.readthedocs.io). To check-out the source code or submit an issue go to [github.com/const-ae/pyLemur](https://github.com/const-ae/pyLemur)
## Citation
> Ahlmann-Eltze C, Huber W (2024).
> “Analysis of multi-condition single-cell data with latent embedding multivariate regression.” bioRxiv.
> [doi:10.1101/2023.03.06.531268](https://doi.org/10.1101/2023.03.06.531268).
# 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](https://pypi.org/project/pyLemur/):
```bash
pip install pyLemur
```
Alternatively, install the latest development version directly from Github:
```bash
pip install git+https://github.com/const-ae/pyLemur.git@main
```
## Documentation
For more information on the functions see the [API docs](https://pyLemur.readthedocs.io/page/api.html) and the [tutorial](https://pylemur.readthedocs.io/page/notebooks/Tutorial.html).
## Contact
For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/const-ae/pyLemur/issues
## Building
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
```