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.

Resources

• 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.

Reference

@article{Birk2024Quantitative,
  title = {Quantitative characterization of cell niches in spatial atlases},
  author = {Birk, S. and others},
  journal = {bioRxiv},
  year = {2024},
  doi = {10.1101/2024.02.21.581428},
  url = {https://www.biorxiv.org/content/10.1101/2024.02.21.581428}
}