Metadata-Version: 2.1
Name: spamosaic
Version: 1.0.3
Summary: SpaMosaic: Mosaic Integration of Spatial Multi-omics
Author-email: Jinmiao Lab <3200376951@qq.com>
License: MIT
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: anndata>=0.9.2
Requires-Dist: scanpy>=1.9.6
Requires-Dist: pandas>=1.5.3
Requires-Dist: h5py>=3.10.0
Requires-Dist: numpy>=1.22.4
Requires-Dist: scikit-learn>=1.3.2
Requires-Dist: seaborn>=0.12.2
Requires-Dist: tqdm>=4.66.1
Requires-Dist: matplotlib>=3.7.4
Requires-Dist: hnswlib
Requires-Dist: annoy
Requires-Dist: PyYAML>=6.0.1
Requires-Dist: networkx>=3.1
Requires-Dist: scipy>=1.10.1

# SpaMosaic

**SpaMosaic** is a Python package for spatial multi-omics data integration using contrastive learning and graph neural networks. It supports integration of partially overlapping modalities and facilitates downstream analyses such as spatial domain identification and modality imputation.

---

## 🔧 Features

- **Horizontal integration**: integrates multiple slices within a single modality
- **Vertical integration**: integrates multiple modalities measured from the same slice
- **Mosaic integration**: integrates multiple slices with overallping modalities 
- **Imputation**: imputes expression profiles of missing omics

---

## 🚀 Installation

### Required Dependencies

SpaMosaic requires external installation of the following packages (not installed automatically):

- PyTorch (version ≥ 2.0)
- PyTorch Geometric (torch-scatter, torch-sparse, etc.)
- harmony-pytorch (version ≥ 0.1.7)

Once these dependencies are installed, simply run:

```bash
pip install spamosaic
```

> ⚠️ Note 
Both CPU and GPU versions of PyTorch and PyTorch Geometric are compatible with SpaMosaic.

## 📚 Documentation
📖 Full tutorials and API reference:
👉 https://spamosaic.readthedocs.io

## 📄 License
SpaMosaic is released under the MIT License.
© 2025 Jinmiao Lab
