Metadata-Version: 2.4
Name: nichecompass
Version: 0.3.2
Summary: End-to-end analysis of spatial multi-omics data
Project-URL: Documentation, https://nichecompass.readthedocs.io/
Project-URL: Source, https://github.com/Lotfollahi-lab/nichecompass
Project-URL: Home-page, https://github.com/Lotfollahi-lab/nichecompass
Author: Sebastian Birk
Maintainer-email: Sebastian Birk <sebastian.birk@outlook.com>
License: BSD 3-Clause License
        
        Copyright (c) 2024, Sebastian Birk, Carlos Talavera-López, Mohammad Lotfollahi
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License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown

<img src="https://github.com/Lotfollahi-lab/nichecompass/blob/main/docs/_static/nichecompass_logo_readme.png" width="800" alt="nichecompass-logo">

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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/).

## Resources
- An installation guide, tutorials and API documentation is available in the [documentation](https://nichecompass.readthedocs.io/).
- Please use [issues](https://github.com/Lotfollahi-lab/nichecompass/issues) to submit bug reports.
- If you would like to contribute, check out the [contributing guide](https://nichecompass.readthedocs.io/en/latest/contributing.html).
- 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}
}
```
