Metadata-Version: 2.3
Name: cat-python
Version: 1.1.0
Summary: Cluster Alignment Tool (CAT)
Project-URL: Documentation, https://brickmanlabcat.readthedocs.io/
Project-URL: Source, https://github.com/brickmanlab/cat-python
Project-URL: Homepage, https://github.com/brickmanlab/cat-python
Author-email: Alex Valentin Nielsen <alexander.nielsen@nbi.ku.dk>, Martin Proks <martin.proks@sund.ku.dk>, Ala Trusina <trusina@nbi.ku.dk>
Maintainer-email: Martin Proks <martin.proks@sund.ku.dk>
License: MIT License
        
        Copyright (c) 2024, Alex Valentin Nielsen, Martin Proks, Ala Trusina
        
        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.
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: anndata
Requires-Dist: plotly
Requires-Dist: polars
Requires-Dist: pyarrow
Requires-Dist: rich
Requires-Dist: rich-argparse
Requires-Dist: xlsxwriter
Provides-Extra: dev
Requires-Dist: pre-commit; extra == 'dev'
Provides-Extra: doc
Requires-Dist: myst-nb>=1.1; extra == 'doc'
Requires-Dist: setuptools; extra == 'doc'
Requires-Dist: sphinx-book-theme>=1; extra == 'doc'
Requires-Dist: sphinx>=4.0; extra == 'doc'
Requires-Dist: sphinxcontrib-bibtex>=1; extra == 'doc'
Description-Content-Type: text/markdown

# Cluster Alignment Tool (CAT)

[![PyPI][pypi-badge]][pypi-link]
[![build][build-badge]][build-link]
[![Documentation][docs-badge]][docs-link]

## Installation

```console
$ pip install cat-python
```

## Installation from source

```console
$ pip install git+https://github.com/brickmanlab/cat-python.git@master
```

## Running CAT

```console
$ catcli \
    --ds1 ./tests/datasets/mock.h5ad \
    --ds1_name DS1 \
    --ds1_cluster Condition_E+D \
    --ds2 ./tests/datasets/mock.h5ad \
    --ds2_name DS2 \
    --ds2_cluster Condition_E+D \
    --output ./res
```

## Build documentation

```console
$ sphinx-build -M html docs docs/_build
```

## Citation

Please consider citing scANVI Explainer if you use in your research.

> Rothová, M.M., Nielsen, A.V., Proks, M. et al. <br>
> Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomics. <br>
> Nat Cell Biol 24, 833–844 (2022). [10.1038/s41556-022-00923-x]

```BibTeX
@article{rothova2022,
  title = {Identification of the Central Intermediate in the Extra-Embryonic to Embryonic Endoderm Transition through Single-Cell Transcriptomics},
  author = {Rothov{\'a}, Michaela Mrugala and Nielsen, Alexander Valentin and Proks, Martin and Wong, Yan Fung and Riveiro, Alba Redo and {Linneberg-Agerholm}, Madeleine and David, Eyal and Amit, Ido and Trusina, Ala and Brickman, Joshua Mark},
  year = {2022},
  month = jun,
  journal = {Nature Cell Biology},
  volume = {24},
  number = {6},
  pages = {833--844},
  publisher = {Nature Publishing Group},
  issn = {1476-4679},
  doi = {10.1038/s41556-022-00923-x}
}

```

[pypi-badge]: https://img.shields.io/pypi/v/cat-python.svg
[pypi-link]: https://pypi.org/project/cat-python
[docs-badge]: https://readthedocs.org/projects/brickmanlabcat/badge/?version=latest
[docs-link]: https://brickmanlabcat.readthedocs.io/en/latest/
[build-badge]: https://github.com/brickmanlab/cat-python/actions/workflows/build.yml/badge.svg
[build-link]: https://github.com/brickmanlab/cat-python/actions/workflows/build.yml
[10.1038/s41556-022-00923-x]: https://doi.org/10.1038/s41556-022-00923-x
