Metadata-Version: 2.4
Name: mintflow
Version: 0.2.0
Summary: Microenvironment-induced and INtrinsic Transcriptomic FLOWs
Project-URL: Documentation, https://mintflow.readthedocs.io/
Project-URL: Source, https://github.com/Lotfollahi-lab/mintflow
Project-URL: Home-page, https://github.com/Lotfollahi-lab/mintflow
Author: Amir Hossein Hosseini Akbarnejad, Sebastian Birk
Maintainer-email: Amir Hossein Hosseini Akbarnejad <aa36@sanger.ac.uk>, Sebastian Birk <sebastian.birk@outlook.com>
License: BSD 3-Clause License
        
        Copyright (c) 2024, Sebastian Birk
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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: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown

<img src="https://github.com/Lotfollahi-lab/mintflow/blob/main/docs/_static/mintflow_logo_readme.png" width="400" alt="mintflow-logo">

[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://github.com/Lotfollahi-lab/mintflow/blob/main/LICENSE)
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MintFlow (**M**icroenvironment-induced and **IN**trinsic **T**ranscriptomic **FLOW**s) is a package to generate disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data. It interoperates with the [scverse](https://scverse.org/) ecosystem to enable seamless analysis workflows of spatial transcriptomics data.

## Installation

Install MintFlow via pip:
```
pip install mintflow
```
For more detailed instructions, visit our [documentation](https://mintflow.readthedocs.io/en/latest/installation.html).

It's highly recommended to setup wandb when training your own MintFlow models.

To do so:
- Go to [wandb](https://wandb.ai/) and create an account.
- Create a project called "MintFlow".

## Resources
- An installation guide, tutorials and API documentation is available in the [documentation](https://mintflow.readthedocs.io/).
- Please use [issues](https://github.com/Lotfollahi-lab/mintflow/issues) to submit bug reports.
- If you would like to contribute, check out the [contributing guide](https://mintflow.readthedocs.io/en/latest/contributing.html).
- If you find MintFlow useful for your research, please consider citing the MintFlow manuscript.

## Reference
```
@article{Akbarnejad2025,
  author    = {Akbarnejad, A. et al.},
  title     = {Mapping and reprogramming microenvironment-induced cell states in human disease using generative AI},
  journal   = {bioRxiv},
  year      = {2025},
  doi       = {10.1101/2025.06.24.661094},
  url       = {https://doi.org/10.1101/2025.06.24.661094}
}
```

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/sebastianbirk/celldino/issues
[changelog]: https://celldino.readthedocs.io/latest/changelog.html
[link-docs]: https://celldino.readthedocs.io
[link-api]: https://celldino.readthedocs.io/latest/api.html
