Metadata-Version: 2.4
Name: spatialleiden
Version: 0.3.0
Summary: Implementation of multiplex Leiden for analysis of (multimodal) spatial omics data.
Author-email: Niklas Müller-Bötticher <niklas.mueller-boetticher@charite.de>, Shashwat Sahay <shashwatsahay.rsg@gmail.com>
License-Expression: MIT
Project-URL: Homepage, https://github.com/HiDiHlabs/SpatialLeiden
Project-URL: Documentation, https://spatialleiden.readthedocs.io
Project-URL: Repository, https://github.com/HiDiHlabs/SpatialLeiden
Project-URL: Issues, https://github.com/HiDiHlabs/SpatialLeiden/issues
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: igraph
Requires-Dist: leidenalg~=0.10.2
Requires-Dist: numpy>=1.21
Requires-Dist: scipy>=1.9
Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Requires-Dist: sphinx-rtd-theme; extra == "docs"
Requires-Dist: anndata>=0.10; extra == "docs"
Requires-Dist: scanpy; extra == "docs"
Requires-Dist: squidpy; extra == "docs"
Requires-Dist: dask<2025; extra == "docs"
Requires-Dist: myst-nb; extra == "docs"
Provides-Extra: dev
Requires-Dist: spatialleiden[docs]; extra == "dev"
Requires-Dist: mudata~=0.3; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Dynamic: license-file

# SpatialLeiden

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/spatialleiden/README.html)


``SpatialLeiden`` is an implementation of
[Multiplex Leiden clustering](https://leidenalg.readthedocs.io/en/stable/multiplex.html)
that can be used to cluster spatially resolved omics data.

``SpatialLeiden`` integrates with the [scverse](https://scverse.org/) by leveraging
[anndata](https://anndata.readthedocs.io/) but can also be used independently.

## Installation

`spatialleiden` is available on [PyPI](https://pypi.org/project/spatialleiden/) and
[bioconda](https://bioconda.github.io/recipes/spatialleiden/README.html).

```sh
# PyPI
pip install spatialleiden
```

```sh
# or conda
conda install bioconda::spatialleiden
```

For detailed installation instructions please refer to the
[documentation](https://spatialleiden.readthedocs.io/page/installation.html).

## Documentation

For documentation of the package please refer to the
[ReadTheDocs page](https://spatialleiden.readthedocs.io/).

## Citations

If you are using `spatialleiden` for your research please cite

Müller-Bötticher, N., Sahay, S., Eils, R., & Ishaque, N. (2025).
SpatialLeiden: spatially aware Leiden clustering.
*Genome Biology*, 26(1), 24. https://doi.org/10.1186/s13059-025-03489-7

```
@article{spatialleiden2025,
	author = {Müller-Bötticher, Niklas and Sahay, Shashwat and Eils, Roland and Ishaque, Naveed},
	title = {SpatialLeiden: spatially aware Leiden clustering},
	journal = {Genome Biology},
	year = {2025},
	month = {Feb},
	day = {07},
	volume = {26},
	number = {1},
	pages = {24},
	doi = {10.1186/s13059-025-03489-7},
	url = {https://doi.org/10.1186/s13059-025-03489-7}
}
```

## Versioning

This project follows the [SemVer](https://semver.org/) guidelines for versioning.

## License

This project is licensed under the MIT License - for details please refer to the
[LICENSE](./LICENSE) file.
