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|Compatible| |PyPI| |PyPiDownloads| |Contributions Welcome| |Build Status|\n|Docs Status| |Pre-commit| |License| |Code Style|\n\n\nscphylo-tools: a python toolkit for single-cell tumor phylogenetic analysis\n===========================================================================\n\n.. image:: https://raw.githubusercontent.com/faridrashidi/scphylo-tools/main/docs/source/_static/images/overview.png\n   :target: https://github.com/faridrashidi/scphylo-tools\n   :alt: overview\n   :align: center\n\n**scphylo-tools** is a comprehensive Python toolkit designed for single-cell tumor\nphylogenetic analysis. It integrates efficient implementations of state-of-the-art\nmethods to infer evolutionary trees from single-cell genotype data.\n\nFeatures\n--------\n\n*   **Phylogenetic Inference**: Wrappers and implementations for state-of-the-art\n    inference methods.\n\n*   **API \u0026 CLI**: Provides a Python API as well as command-line tools.\n\n*   **Visualization**: Built-in visualization tools.\n\n*   **Datasets**: Access to available datasets.\n\n*   **Ease of Use**: A unified Python interface for complex phylogenetic workflows.\n\nInstallation\n------------\n\nInstall the package via pip:\n\n.. code-block:: bash\n\n    pip install scphylo-tools\n\nDocumentation\n-------------\n\nDetailed documentation and tutorials are available at `Read the Docs \u003chttps://scphylo-tools.readthedocs.io\u003e`_.\n\n.. Citation\n.. --------\n\n.. If you use ``scphylo-tools`` in your research, please cite the DOI linked above.\n\n\n.. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2021.03.26.437185-orange?logo=gitbook\u0026logoColor=FFFFFF\u0026style=flat-square\n    :target: https://doi.org/10.1101/2021.03.26.437185\n    :alt: DOI\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/scphylo-tools?logo=PyPi\u0026logoColor=FFFFFF\u0026style=flat-square\u0026color=blue\n    :target: https://pypi.org/project/scphylo-tools\n    :alt: PyPI\n\n.. |PyPyDownloads| image:: https://img.shields.io/badge/dynamic/json?logo=PyPi\u0026logoColor=FFFFFF\u0026style=flat-square\u0026color=blue\u0026label=downloads\u0026query=%24.total_downloads\u0026url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fscphylo-tools\n    :target: https://pepy.tech/project/scphylo-tools\n    :alt: PyPyDownloads\n\n.. |PyPiDownloads| image:: https://img.shields.io/pypi/dm/scphylo-tools.svg?logo=docusign\u0026logoColor=FFFFFF\u0026style=flat-square\u0026color=blue\n    :target: https://pepy.tech/project/scphylo-tools\n    :alt: PyPiDownloads\n\n.. |Stars| image:: https://img.shields.io/github/stars/faridrashidi/scphylo-tools?logo=GitHub\u0026color=yellow\u0026style=flat-square\n    :target: https://github.com/faridrashidi/scphylo-tools\n    :alt: Stars\n\n.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions\u0026message=welcome\u0026color=0059b3\u0026logo=handshake\u0026logoColor=FFFFFF\u0026style=flat-square\n    :target: https://github.com/faridrashidi/scphylo-tools/blob/master/CONTRIBUTING.rst\n    :alt: Contributions Welcome\n\n.. |Compatible| image:: https://img.shields.io/pypi/pyversions/scphylo-tools.svg?logo=python\u0026logoColor=FFFFFF\u0026style=flat-square\u0026color=blue\n    :target: https://pypi.org/project/scphylo-tools\n    :alt: Compatible\n\n.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/faridrashidi/scphylo-tools/ci.yml?branch=main\u0026label=build\u0026logo=githubactions\u0026logoColor=FFFFFF\u0026style=flat-square\n    :target: https://github.com/faridrashidi/scphylo-tools/actions?query=workflow%3ACI\n    :alt: Build Status\n\n.. |Docs Status| image:: https://img.shields.io/readthedocs/scphylo-tools/latest?logo=readthedocs\u0026logoColor=FFFFFF\u0026style=flat-square\n    :target: https://scphylo-tools.readthedocs.io\n    :alt: Docs Status\n\n.. |Pre-commit| image:: https://img.shields.io/badge/pre--commit.ci-passing-brightgreen?logo=pre-commit\u0026logoColor=white\u0026style=flat-square\n    :target: https://results.pre-commit.ci/latest/github/faridrashidi/scphylo-tools/master\n    :alt: Pre-commit\n\n.. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg?logo=visualstudiocode\u0026logoColor=FFFFFF\u0026style=flat-square\n    :target: https://github.com/python/black\n    :alt: Code Style\n\n.. |Code Score| image:: https://img.shields.io/lgtm/grade/python/github/faridrashidi/scphylo-tools.svg?logo=lgtm\u0026logoWidth=18\u0026style=flat-square\n    :target: https://lgtm.com/projects/g/faridrashidi/scphylo-tools/context:python\n    :alt: Code Score\n\n.. |Codecov| image:: https://img.shields.io/codecov/c/github/faridrashidi/scphylo-tools?logo=codecov\u0026logoColor=white\u0026style=flat-square\n    :target: https://codecov.io/gh/faridrashidi/scphylo-tools\n    :alt: Codecov\n\n.. |License| image:: https://img.shields.io/pypi/l/scphylo-tools.svg?logo=creativecommons\u0026logoColor=FFFFFF\u0026style=flat-square\u0026color=blueviolet\n    :target: https://github.com/faridrashidi/scphylo-tools/blob/main/LICENSE\n    :alt: License\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffaridrashidi%2Fscphylo-tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffaridrashidi%2Fscphylo-tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffaridrashidi%2Fscphylo-tools/lists"}