SPCoral is a Python package designed for diagonal integration of spatial multi-omics data from adjacent tissue slices. It comprises two modules: Alignment and Integration. The alignment module employs graph neural networks and Gromov-Wasserstein optimal transport to perform slice-to-slice positional alignment without relying on shared molecular features. The integration module builds upon these aligned coordinates, using a cross-modal attention mechanism to fuse molecular features across different modalities and resolutions. SPCoral supports a variety of downstream applications, including spatial domain identification, cross-omics prediction, spatial cell-cell communication inference, and other spatial multi-omics analyses.
pip:
pip install spcoral
github:
cd spcoral
python setup.py build
python setup.py install