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scphylo-tools: a python toolkit for single-cell tumor phylogenetic analysis
===========================================================================

.. image:: https://raw.githubusercontent.com/faridrashidi/scphylo-tools/main/docs/source/_static/images/overview.png
   :target: https://github.com/faridrashidi/scphylo-tools
   :alt: overview
   :align: center

**scphylo-tools** is a comprehensive Python toolkit designed for single-cell tumor
phylogenetic analysis. It integrates efficient implementations of state-of-the-art
methods to infer evolutionary trees from single-cell genotype data.

Features
--------

*   **Phylogenetic Inference**: Wrappers and implementations for state-of-the-art
    inference methods.

*   **API & CLI**: Provides a Python API as well as command-line tools.

*   **Visualization**: Built-in visualization tools.

*   **Datasets**: Access to available datasets.

*   **Ease of Use**: A unified Python interface for complex phylogenetic workflows.

Installation
------------

Install the package via pip:

.. code-block:: bash

    pip install scphylo-tools

Documentation
-------------

Detailed documentation and tutorials are available at `Read the Docs <https://scphylo-tools.readthedocs.io>`_.

.. Citation
.. --------

.. If you use ``scphylo-tools`` in your research, please cite the DOI linked above.


.. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2021.03.26.437185-orange?logo=gitbook&logoColor=FFFFFF&style=flat-square
    :target: https://doi.org/10.1101/2021.03.26.437185
    :alt: DOI

.. |PyPI| image:: https://img.shields.io/pypi/v/scphylo-tools?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue
    :target: https://pypi.org/project/scphylo-tools
    :alt: PyPI

.. |PyPyDownloads| image:: https://img.shields.io/badge/dynamic/json?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fscphylo-tools
    :target: https://pepy.tech/project/scphylo-tools
    :alt: PyPyDownloads

.. |PyPiDownloads| image:: https://img.shields.io/pypi/dm/scphylo-tools.svg?logo=docusign&logoColor=FFFFFF&style=flat-square&color=blue
    :target: https://pepy.tech/project/scphylo-tools
    :alt: PyPiDownloads

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    :target: https://github.com/faridrashidi/scphylo-tools
    :alt: Stars

.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=0059b3&logo=handshake&logoColor=FFFFFF&style=flat-square
    :target: https://github.com/faridrashidi/scphylo-tools/blob/master/CONTRIBUTING.rst
    :alt: Contributions Welcome

.. |Compatible| image:: https://img.shields.io/pypi/pyversions/scphylo-tools.svg?logo=python&logoColor=FFFFFF&style=flat-square&color=blue
    :target: https://pypi.org/project/scphylo-tools
    :alt: Compatible

.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/faridrashidi/scphylo-tools/ci.yml?branch=main&label=build&logo=githubactions&logoColor=FFFFFF&style=flat-square
    :target: https://github.com/faridrashidi/scphylo-tools/actions?query=workflow%3ACI
    :alt: Build Status

.. |Docs Status| image:: https://img.shields.io/readthedocs/scphylo-tools/latest?logo=readthedocs&logoColor=FFFFFF&style=flat-square
    :target: https://scphylo-tools.readthedocs.io
    :alt: Docs Status

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    :alt: Pre-commit

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    :target: https://github.com/python/black
    :alt: Code Style

.. |Code Score| image:: https://img.shields.io/lgtm/grade/python/github/faridrashidi/scphylo-tools.svg?logo=lgtm&logoWidth=18&style=flat-square
    :target: https://lgtm.com/projects/g/faridrashidi/scphylo-tools/context:python
    :alt: Code Score

.. |Codecov| image:: https://img.shields.io/codecov/c/github/faridrashidi/scphylo-tools?logo=codecov&logoColor=white&style=flat-square
    :target: https://codecov.io/gh/faridrashidi/scphylo-tools
    :alt: Codecov

.. |License| image:: https://img.shields.io/pypi/l/scphylo-tools.svg?logo=creativecommons&logoColor=FFFFFF&style=flat-square&color=blueviolet
    :target: https://github.com/faridrashidi/scphylo-tools/blob/main/LICENSE
    :alt: License
