Metadata-Version: 2.1
Name: scanpex
Version: 0.2.1
Summary: ScanPy Extension and kwarg Preferences
Author: yo-aka-gene
Author-email: yujiokano@keio.jp
Requires-Python: >=3.10,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: anndata (<0.12)
Requires-Dist: fastcluster (>=1.3.0,<2.0.0)
Requires-Dist: jax (<0.5.0)
Requires-Dist: jaxlib (<0.5.0)
Requires-Dist: matplotlib (>=3.10.8,<4.0.0)
Requires-Dist: mygene (>=3.2.2,<4.0.0)
Requires-Dist: numba (==0.60.0)
Requires-Dist: numpy (<2.1)
Requires-Dist: pandas (>=1.5.3)
Requires-Dist: scanpy (>=1.11.5,<2.0.0)
Requires-Dist: scikit-learn (<1.8)
Requires-Dist: scipy (<1.16)
Requires-Dist: seaborn (>=0.13.2,<0.14.0)
Requires-Dist: seacells (>=0.3.3,<0.4.0)
Description-Content-Type: text/markdown

<img src="https://raw.githubusercontent.com/yo-aka-gene/ScanpEx/main/docs/_static/scanpex_title.png"> 

# ScanpEx
[<img src="https://img.shields.io/badge/GitHub-yo--aka--gene/ScanpEx-181717?style=flat&logo=github">](https://github.com/yo-aka-gene/ScanpEx)
[![Documentation Status](https://readthedocs.org/projects/scanpex/badge/?version=latest)](https://scanpex.readthedocs.io/en/latest/?badge=latest)
[<img src="https://img.shields.io/badge/Documentation-scanpex.rtfd.io-8CA1AF?style=flat&logo=readthedocs">](https://scanpex.readthedocs.io/en/latest/)
<img src="https://img.shields.io/badge/Python-3.10%2B-3776AB?style=flat&logo=python">
[![PyPi](https://img.shields.io/pypi/v/scanpex?logo=pypi&label=PyPI&color=3775A9)](https://pypi.org/project/scanpex)

- ScanPy Extension and kwarg Preferences
- Most codes were initially employed in ["Design-of-Experiments for Nonlinear, Multivariate Biology: Rethinking Experimental Design through Perturb-seq"](https://www.biorxiv.org/content/10.64898/2025.12.28.696309v2)
- Related repositories:
    - [<img src="https://img.shields.io/badge/GitHub-yo--aka--gene/WhyDOE-181717?style=flat&logo=github">](https://github.com/yo-aka-gene/WhyDOE)
    - [<img src="https://img.shields.io/badge/GitHub-yo--aka--gene/WhyDOE_RWD_Analysis-181717?style=flat&logo=github">](https://github.com/yo-aka-gene/WhyDOE_RWD_Analysis)

## Documentation
Visit [https://scanpex.readthedocs.io/en/latest/](https://scanpex.readthedocs.io/en/latest/)

## Installation
```
pip install scanpex
```

## Citation
```
@article{okano2025design,
  title={Design-of-Experiments for Nonlinear, Multivariate Biology: Rethinking Experimental Design through Perturb-seq},
  author={Okano, Yuji and Ishikawa, Tetsuo and Sato, Yasunori and Okano, Hideyuki and Sakurada, Kazuhiro},
  journal={bioRxiv},
  pages={2025--12},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}
```

