Metadata-Version: 2.4
Name: pertpy
Version: 0.10.0
Summary: Perturbation Analysis in the scverse ecosystem.
Project-URL: Documentation, https://pertpy.readthedocs.io
Project-URL: Source, https://github.com/scverse/pertpy
Project-URL: Home-page, https://github.com/scverse/pertpy
Author: Lukas Heumos, Yuge Ji, Lilly May, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Tessa Green, Stefan Peidli, Antonia Schumacher, Gregor Sturm
Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
License: MIT License
        
        Copyright (c) 2021, Lukas Heumos
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
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Description-Content-Type: text/markdown

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# pertpy

![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)

## Documentation

Please read the [documentation](https://pertpy.readthedocs.io/en/latest).

## Installation

We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
No particular hardware beyond a standard laptop is required.

You can install _pertpy_ in less than a minute via [pip] from [PyPI]:

```console
pip install pertpy
```

if you want to use scCODA or tascCODA, please install pertpy as follows:

```console
pip install 'pertpy[coda]'
```

If you want to use the differential gene expression interface, please install pertpy by running:

```console
pip install 'pertpy[de]'
```

## Citation

[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)

[pip]: https://pip.pypa.io/
[pypi]: https://pypi.org/
[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
