Metadata-Version: 2.4
Name: cyclevi
Version: 0.1.1
Summary: CycleVI: Isolating cell cycle variation with an interpretable deep generative model
Author: Pia Mozdzanowski, Marcel Tarbier, Gustavo S. Jeuken
License: BSD 3-Clause License
        
        Copyright (c) 2025, Gustavo Jeuken
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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Project-URL: Homepage, https://github.com/jeuken/CycleVI
Project-URL: Bug Tracker, https://github.com/jeuken/CycleVI/issues
Project-URL: Preprint, https://doi.org/10.1101/2025.11.04.686009
Keywords: single-cell,cell cycle,variational autoencoder,scRNA-seq,deep learning
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: torch>=2.0
Requires-Dist: numpy>=1.23
Requires-Dist: pandas>=1.5
Requires-Dist: anndata>=0.9
Requires-Dist: scvi-tools>=1.1
Dynamic: license-file

# CycleVI

## Overview
This repository contains the source code for the CycleVI method, as presented in [our preprint](https://doi.org/10.1101/2025.11.04.686009)

## Dependencies

* scvi-tools
* anndata
* PyTorch

## Structure

* [CycleVI_model](CycleVI_model.py): model implementation.
* [Tutorial](Tutorial.ipynb): a python notebook with ans example on how to run the model.
* [Tutorial_colab](Tutorial_colab.ipynb): same tutorial, but ready to run on Google Colab.

## Installation

```bash
pip install cyclevi
```

## Usage

```python
from cyclevi import CycleVI
```

Instructions on how to use the model are present in the ``Tutorial.ipynb`` notebook.

## Feedback
For questions and comments, feel free to contact [Gustavo S. Jeuken](mailto:g.stolfjeuken@vu.nl).

## License
BSD 3-Clause License

## Citation
If you use this model in a publication, please cite [our preprint](https://doi.org/10.1101/2025.11.04.686009)

>CycleVI: Isolating cell cycle variation with an interpretable deep generative model
>
>Pia Mozdzanowski, Marcel Tarbier, Gustavo S. Jeuken
>
>bioRxiv 2025.11.04.686009; doi: https://doi.org/10.1101/2025.11.04.686009
