nichecompass

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{Birk2025,
  author    = {Birk, S. et al.},
  title     = {Quantitative characterization of cell niches in spatially resolved omics data},
  journal   = {Nature Genetics},
  year      = {2025},
  doi       = {10.1038/s41588-025-02120-6},
  url       = {https://doi.org/10.1038/s41588-025-02120-6}
}

Development Status
- 3 - Alpha
Intended Audience
- Science/Research
Natural Language
- English
Operating System
- POSIX :: Linux
Programming Language
- Python :: 3.10
Topic
- Scientific/Engineering :: Bio-Informatics

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nichecompass-0.3.3.tar.gz (39.6 MB view details)

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- Permalink: Lotfollahi-lab/nichecompass@5bf7d2a09e70bd490c59e978e37f4df30f812994
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