Metadata-Version: 2.4
Name: interscale
Version: 0.0.1
Summary: Multi-scale cell interaction model for spatial transcriptomics data.
Project-URL: Documentation, https://icb-interscale.readthedocs.io/
Project-URL: Homepage, https://github.com/theislab/interscale
Project-URL: Source, https://github.com/theislab/interscale
Author: Francesca Drummer, Sara Jimenez
Maintainer-email: Francesca Drummer <Francesca.Drummer@helmholtz-munich.de>
License-Expression: BSD-3-Clause
License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.11
Requires-Dist: anndata
Requires-Dist: fast-array-utils[accel]
Requires-Dist: geome
Requires-Dist: lightning>=2
Requires-Dist: numpy>=1.19
Requires-Dist: pandas
Requires-Dist: scanpy
Requires-Dist: scikit-learn
Requires-Dist: scipy>=1.7
Requires-Dist: scvi-tools>=0.19
Requires-Dist: session-info2
Requires-Dist: squidpy>=1.7
Requires-Dist: torch-geometric>=2
Requires-Dist: torch>=2
Requires-Dist: torchmetrics>=1.8
Requires-Dist: wandb
Requires-Dist: yacs
Description-Content-Type: text/markdown

# InterScale

[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://github.com/theislab/interscale/blob/main/LICENSE)
[![Stars](https://img.shields.io/github/stars/Lotfollahi-lab/interscale?logo=GitHub&color=yellow)](https://github.com/Lotfollahi-lab/interscale/stargazers)
[![PyPI](https://img.shields.io/pypi/v/interscale.svg)](https://pypi.org/project/interscale)
[![PyPIDownloads](https://static.pepy.tech/badge/interscale)](https://pepy.tech/project/interscale)
[![Docs](https://readthedocs.org/projects/interscale/badge/?version=latest)](https://interscale.readthedocs.io/en/stable/?badge=stable)
[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)

![InterScale concept](docs/_static/img/InterScale_concept.png)

InterScale is a package for cell interaction analysis in spatial transcriptomics data. It is build on top of PyG (via geome), AnnData, scanpy squidpy and scvi-tools.

## Resources
- An installation guide, tutorials and API documentation is available in the [documentation](https://interscale.readthedocs.io/).
- Check out our seperate [reproduciblity repository](https://github.com/theislab/InterScale_reproducibility/) to reproduce the figures for the manuscript
- Please use [issues](https://github.com/theislab/interscale/issues) to submit bug reports.
- If you would like to contribute, check out the [contributing guide](https://interscale.readthedocs.io/en/latest/contributing.html).
- If you find InterScale useful for your research, please consider citing the InterScale preprint.

## Reference

```
@article{DrummerJimenez2026,
  author    = {Drummer, F. and Jimenez, S. et al.},
  title     = {InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics},
  journal   = {BioArvix},
  year      = {2026},
  doi       = {???},
  url       = {???}
}
```
