Metadata-Version: 2.4
Name: epione
Version: 0.0.1rc1
Summary: EpiOne: Generative cartography of single-cell epigenomes
Keywords: bioinformatics,deep-learning,single-cell,ATAC-seq
Author-email: Zehua Zeng <starlitnightly@gmail.com>
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
Requires-Dist: muon>=0.1
Requires-Dist: pyBigWig>=0.3
Requires-Dist: loompy>=3.0.7
Requires-Dist: pyrange
Requires-Dist: MOODS-python ; extra == "full"
Requires-Dist: pysam ; extra == "full"
Requires-Dist: pynndescent ; extra == "full"
Requires-Dist: pyjaspar ; extra == "full"
Requires-Dist: omicverse ; extra == "full"
Project-URL: Github, https://github.com/aristoteleo/epione
Provides-Extra: full

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<p align="center">
  <img src="epione_guide/_static/logo.png" alt="Epione Logo" width="400"/>
</p>

<div align="center">

# Epione

***Generative Cartography of Single-Cell Epigenomes***

**A Python framework for single-cell epigenomic analysis**

[![][github-release-shield]][github-release-link]
[![][python-shield]][python-link]
[![][license-shield]][license-link]<br/>
[![][github-contributors-shield]][github-contributors-link]
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[![Python 3.9+](https://img.shields.io/badge/python-3.9%2B-blue.svg)](https://www.python.org/downloads/)
[![Status: Early Development](https://img.shields.io/badge/Status-Early%20Development-orange.svg)]()
[![Single-Cell](https://img.shields.io/badge/Single--Cell-Epigenomics-purple.svg)]()

</div>

## What is Epione?

**Epione** is a Python framework for **single-cell epigenomic analysis** and **generative modeling**. Named after the Greek goddess of healing, Epione aims to provide tools for understanding epigenomic landscapes in single cells.

> ⚠️ **Version 0.0.1**: This is an early development version. Core features are still being implemented.

## Installation

**From source:**
```bash
git clone https://github.com/aristoteleo/epione.git
cd epione
pip install -e .
```

> 📋 PyPI release coming in future versions

## Basic Usage

```python
import epione as epi

# Basic functionality coming soon
# Check documentation for current capabilities
```

## Requirements

- Python 3.9+
- Core dependencies:
  - `numpy`, `pandas`, `scipy`
  - `anndata`
  - Additional dependencies will be defined as features are implemented

## Documentation

Documentation is being developed and will be available at the project website. Current documentation drafts are in the `epione_guide/` directory.

## Development Status

**Version 0.0.1** includes:
- Project structure and basic setup
- Initial documentation framework
- Core package skeleton

**Coming in future versions:**
- Single-cell data processing utilities
- Generative modeling tools
- Visualization functions
- Comprehensive tutorials and examples

## Contributing

This project is in early development. We welcome:

- Feature suggestions and feedback
- Bug reports and issues
- Documentation improvements
- Code contributions

## License

This project is [GPL 3.0](./LICENSE) licensed.

---

**Built for the single-cell epigenomics community**

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[github-contributors-shield]: https://img.shields.io/github/contributors/aristoteleo/epione?color=c4f042&labelColor=black&style=flat-square
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[python-link]: https://www.python.org/
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