Metadata-Version: 2.4
Name: atac-mapper
Version: 0.1.0
Summary: Map query scATAC-seq data to a single-cell chromatin accessibility atlas
Author: Nadezhda Azbukina
Maintainer-email: Nadezhda Azbukina <nazbukina@ethz.ch>
License: MIT License
        
        Copyright (c) 2025, QuadBio Lab
        
        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
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Classifier: Programming Language :: Python :: 3 :: Only
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: Programming Language :: Python :: 3.13
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: cellmapper>=0.1
Requires-Dist: cloudpickle>=2.2
Requires-Dist: joblib>=1.3
Requires-Dist: numpy>=1.24
Requires-Dist: pandas>=2
Requires-Dist: scanpy>=1.11
Requires-Dist: scarches>=0.5
Requires-Dist: scipy>=1.11
Requires-Dist: scvi-tools>=1
Requires-Dist: torch>=2
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: pytest>=7; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Provides-Extra: doc
Requires-Dist: myst-nb>=1; extra == "doc"
Requires-Dist: sphinx>=8; extra == "doc"
Requires-Dist: sphinx-autodoc-typehints>=3; extra == "doc"
Requires-Dist: sphinx-book-theme>=1.1; extra == "doc"
Requires-Dist: sphinx-copybutton; extra == "doc"
Requires-Dist: sphinx-tabs; extra == "doc"
Requires-Dist: sphinxcontrib-bibtex>=2.6; extra == "doc"
Requires-Dist: sphinxext-opengraph; extra == "doc"
Provides-Extra: test
Requires-Dist: pytest>=7; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Dynamic: license-file

# Atac Mapper

[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/quadbio/atac_mapper/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/atac_mapper

Map query scATAC-seq data to a single-cell chromatin accessibility atlas using cisTopics.

## Getting started

Please refer to the [documentation][],
in particular, the [API documentation][].

## Installation

You need to have Python 3.10 or newer installed on your system.
If you don't have Python installed, we recommend installing [uv][].

There are several alternative options to install atac_mapper:

<!--
1) Install the latest release of `atac_mapper` from [PyPI][]:

```bash
pip install atac_mapper
```
-->

1. Install the latest development version:

```bash
pip install git+https://github.com/quadbio/atac_mapper.git@main
```

## Release notes

See the [changelog][].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][].
If you found a bug, please use the [issue tracker][].

## Citation

If you find AtacMapper useful in your research, please, cite the following article:

```bibtex
@article{azbukina2025multiomic,
  title={Multi-omic human neural organoid cell atlas of the posterior brain},
  author={Azbukina, Nadezhda and He, Zhisong and Lin, Hsiu-Chuan and Santel, Malgorzata and Kashanian, Bijan and Maynard, Ashley and T{\"o}r{\"o}k, Tivadar and Okamoto, Ryoko and Nikolova, Marina and Kanton, Sabina and Br{\"o}samle, Valentin and Holtackers, Rene and Camp, J Gray and Treutlein, Barbara},
  journal={bioRxiv},
  pages={2025--03},
  year={2025},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2025.03.20.644368}
}
```

[uv]: https://github.com/astral-sh/uv
[scverse discourse]: https://discourse.scverse.org/
[issue tracker]: https://github.com/quadbio/atac_mapper/issues
[tests]: https://github.com/quadbio/atac_mapper/actions/workflows/test.yaml
[documentation]: https://atac-mapper.readthedocs.io/en/latest/index.html
[changelog]: https://atac_mapper.readthedocs.io/en/latest/changelog.html
[api documentation]: https://atac-mapper.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/atac_mapper

<!-- Example of additional links you might want to add -->
[bioRxiv paper]: https://www.biorxiv.org/content/10.1101/2025.03.20.644368v1
[quadbio lab]: https://github.com/quadbio
[scanpy]: https://scanpy.readthedocs.io/
[scvi-tools]: https://docs.scvi-tools.org/
