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}
}
1 maintainer
Metadata
1 maintainer
Release files for nichecompass 0.3.3
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Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| nichecompass-0.3.3.tar.gz | 39.6 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| nichecompass-0.3.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 39.8 MB
Release files / nichecompass-0.3.3.tar.gz
| Download URL | nichecompass-0.3.3.tar.gz |
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| Size | 39.6 MB |
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| Size | 126.7 kB |
| Tags | Python 3 |
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