https://github.com/const-ae/pylemur
A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.7%) to scientific vocabulary
Repository
A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
Basic Info
- Host: GitHub
- Owner: const-ae
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://pylemur.readthedocs.io/
- Size: 3.24 MB
Statistics
- Stars: 26
- Watchers: 2
- Forks: 4
- Open Issues: 1
- Releases: 3
Metadata Files
README.md
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:
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 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
Owner
- Name: Constantin
- Login: const-ae
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL
- Website: https://twitter.com/const_ae
- Repositories: 64
- Profile: https://github.com/const-ae
PhD Student, Biostats, R
GitHub Events
Total
- Create event: 2
- Release event: 2
- Issues event: 4
- Watch event: 15
- Issue comment event: 5
- Push event: 5
- Pull request event: 3
Last Year
- Create event: 2
- Release event: 2
- Issues event: 4
- Watch event: 15
- Issue comment event: 5
- Push event: 5
- Pull request event: 3
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 4
- Average time to close issues: about 14 hours
- Average time to close pull requests: 1 day
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 2.33
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: about 20 hours
- Average time to close pull requests: 35 minutes
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 2.5
- Average comments per pull request: 0.5
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dglubokov (1)
- krademaker (1)
- grst (1)
Pull Request Authors
- keller-mark (2)
- Intron7 (2)
- scverse-bot (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 32 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
pypi.org: pylemur
A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
- Documentation: https://pyLemur.readthedocs.io/
- License: MIT License Copyright (c) 2024, Your Name Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.3.1
published over 1 year ago