NicheCompass (Niche Identification based on Cellular grapH Embeddings of COMmunication Programs Aligned across Spatial Samples) is a package for end-to-end analysis of spatial multi-omics data, including spatial atlas building, niche identification & characterization, cell-cell communication inference and spatial reference mapping. It is built on top of PyG and AnnData.
- An installation guide, tutorials and API documentation is available in the documentation.
- Please use issues to submit bug reports.
- If you would like to contribute, check out the contributing guide.
- If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.