Metadata-Version: 2.2
Name: stEDGE
Version: 1.1.2
Summary: Edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics
Author-email: Yi He <yihe_csu@csu.edu.cn>
License: MIT
Project-URL: Homepage, https://github.com/yihe-csu/stEDGE
Project-URL: Documentation, https://stedge-tutorials.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/yihe-csu/stEDGE
Project-URL: Tutorials, https://github.com/yihe-csu/stEDGE_Tutorials
Keywords: spatial transcriptomics,spatial domains,tissue architecture,transition interfaces,gene programs
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.26
Requires-Dist: pandas>=2.1
Requires-Dist: scipy>=1.11
Requires-Dist: scikit-learn>=1.3
Requires-Dist: anndata>=0.10
Requires-Dist: scanpy>=1.10
Requires-Dist: squidpy>=1.4
Requires-Dist: networkx>=3.0
Requires-Dist: igraph>=0.11
Requires-Dist: leidenalg>=0.10
Requires-Dist: POT>=0.9
Requires-Dist: joblib>=1.3
Requires-Dist: tqdm>=4.66
Requires-Dist: kneed>=0.8
Requires-Dist: matplotlib>=3.8
Requires-Dist: seaborn>=0.13
Requires-Dist: statsmodels>=0.14

<p align="center">
  <img src="https://raw.githubusercontent.com/yihe-csu/stEDGE/main/docs/Logo.png" alt="stEDGE logo" width="45%">
</p>

# stEDGE

[![Documentation Status](https://readthedocs.org/projects/stedge-tutorials/badge/?version=latest)](https://stedge-tutorials.readthedocs.io/en/latest/)

**stEDGE** is an edge-guided and interpretable framework for reconstructing multiscale tissue architecture from spatial transcriptomics data.

stEDGE models local boundary probability and domain transition intensity to identify stable compartments, transition-rich interfaces, and hierarchical spatial states.

## Installation

Install stEDGE from PyPI:

```bash
pip install stEDGE
```

## Documentation

Online documentation and tutorials are available at:

https://stedge-tutorials.readthedocs.io/en/latest/

The source code is available at:

https://github.com/yihe-csu/stEDGE

The tutorial source repository is available at:

https://github.com/yihe-csu/stEDGE_Tutorials

## Main features

- Edge-guided reconstruction of fine-grained spatial domains
- Boundary probability and transition interface analysis
- Multiscale hierarchy construction across fine, domain, and coarse levels
- Tree-guided spatial gene program interpretation
- Applications to Visium, Slide-seqV2, Xenium, and other spatial transcriptomics data

## Citation

If you use `stEDGE` in your work, please cite:

He, Y. **stEDGE enables edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics**. 2026.

Citation information will be updated upon publication.
