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NicheCompass (**N**iche **I**dentification based on **C**ellular grap**H** **E**mbeddings of **COM**munication **P**rograms **A**ligned across **S**patial **S**amples) 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](https://pytorch-geometric.readthedocs.io/en/latest/) and [AnnData](https://anndata.readthedocs.io/en/latest/).

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NicheCompass (**N**iche **I**dentification based on **C**ellular grap**H** **E**mbeddings of **COM**munication **P**rograms **A**ligned across **S**patial **S**amples) 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](https://pytorch-geometric.readthedocs.io/en/latest/) and [AnnData](https://anndata.readthedocs.io/en/latest/).





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## Resources

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## Resources






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- An installation guide, tutorials and API documentation is available in the [documentation](https://nichecompass.readthedocs.io/).

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- An installation guide, tutorials and API documentation is available in the [documentation](https://nichecompass.readthedocs.io/).






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- Please use [issues](https://github.com/Lotfollahi-lab/nichecompass/issues) to submit bug reports.

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- Please use [issues](https://github.com/Lotfollahi-lab/nichecompass/issues) to submit bug reports.






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- If you would like to contribute, check out the [contributing guide](https://nichecompass.readthedocs.io/en/latest/contributing.html).

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- If you would like to contribute, check out the [contributing guide](https://nichecompass.readthedocs.io/en/latest/contributing.html).






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- If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.

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- If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.





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## Reference

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## Reference






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```

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```






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@article{Birk2025,

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@article{Birk2025,






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  author    = {Birk, S. and Bonafonte-Pard{\`a}s, I. and Feriz, A. M. and et al.},

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  author    = {Birk, S. and Bonafonte-Pard{\`a}s, I. and Feriz, A. M. and et al.},






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  title     = {Quantitative characterization of cell niches in spatially resolved omics data},

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  title     = {Quantitative characterization of cell niches in spatially resolved omics data},






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  journal   = {Nature Genetics},

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  journal   = {Nature Genetics},






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  year      = {2025},

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  year      = {2025},






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  doi       = {10.1038/s41588-025-02120-6},

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  doi       = {10.1038/s41588-025-02120-6},






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  url       = {https://doi.org/10.1038/s41588-025-02120-6}

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  url       = {https://doi.org/10.1038/s41588-025-02120-6}






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}

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}






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```

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```