https://github.com/lueckenlab/patpy
Toolbox for single-cell data analysis on sample level
https://github.com/lueckenlab/patpy
compbio single-cell-rna-seq
Last synced: 5 months ago
JSON representation
Toolbox for single-cell data analysis on sample level
- Host: GitHub
- URL: https://github.com/lueckenlab/patpy
- Owner: lueckenlab
- License: bsd-3-clause
- Created: 2023-05-08T13:44:56.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-12-15T18:14:00.000Z (6 months ago)
- Last Synced: 2025-12-19T01:19:02.650Z (6 months ago)
- Topics: compbio, single-cell-rna-seq
- Language: Python
- Homepage:
- Size: 40.4 MB
- Stars: 8
- Watchers: 0
- Forks: 5
- Open Issues: 26
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# patpy – sample-level analysis framework for single-cell data
patpy is a toolbox for single-cell data analysis on sample level.
It provides:
- 👨⚕️ Interface to sample representation methods (otherwise known as patient representation)
- 📈 Analysis functions to get the most of your data
- 📊 Metrics for sample representation evaluation
# ⚠️ Warning: Development in Progress ⚠️
> **This repository is currently under active development**
> Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.
---
**Please proceed with caution** and feel free to contribute, but be aware that:
- The codebase is still evolving.
- Documentation may be incomplete.
- Some features may be unstable or subject to change.
If you have any questions or face bugs, feel free to open an [issue](https://github.com/lueckenlab/patpy/issues).
Thank you for your patience and interest. Stay tuned for updates!
---
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/lueckenlab/patpy/test.yaml?branch=main
[link-tests]: https://github.com/lueckenlab/patpy/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/patpy
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api].
## Installation
You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install patpy:
1. Install the latest release of `patpy` from [`PyPI`](https://pypi.org/project/patpy/):
```bash
pip install patpy
```
2. Install the latest development version:
```bash
pip install git+https://github.com/lueckenlab/patpy.git@main
```
To install specific dependencies for some sample representation tools, use the following command:
```bash
pip install patpy[pilot]
```
All the available dependency groups: `diffusionemd`, `mrvi`, `pilot`, `scpoli`, `wassersteintsne`.
## Release notes
See the [changelog][changelog].
## 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].
## Building docs
1. Install [sphinx](https://www.sphinx-doc.org/en/master/usage/installation.html)
You may need add path to `sphinx-doc` to the `$PATH`
2. Install other `doc` section dependencies from the [pyproject.toml](https://github.com/lueckenlab/patpy/blob/main/pyproject.toml)
3. Build the documentation pages:
```bash
cd docs
make html
```
4. Open `docs/_build/html/index.html`
## Citation
Preprint is coming soon. So far, you can refer to this repository as following:
### APA
Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/
### BibTeX
```bibtex
@misc{shitov_patpy_2024,
author = {Shitov, Vladimir},
title = {patpy – sample-level analysis framework for single-cell data},
year = {2024},
url = {https://github.com/lueckenlab/patpy/},
note = {Version 0.11.3}
}
```
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/lueckenlab/patpy/issues
[changelog]: https://patpy.readthedocs.io/en/latest/changelog.html
[link-docs]: https://patpy.readthedocs.io
[link-api]: https://patpy.readthedocs.io/en/latest/api/index.html