https://github.com/faridrashidi/scphylo-tools

a python toolkit for single-cell tumor phylogenetic analysis
https://github.com/faridrashidi/scphylo-tools

algorithms bioinformatics cancer computational-biology evolution phylogenetics single-cell

Last synced: 6 months ago
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a python toolkit for single-cell tumor phylogenetic analysis

• Host: GitHub
• URL: https://github.com/faridrashidi/scphylo-tools
• Owner: faridrashidi
• License: bsd-3-clause
• Created: 2021-12-07T01:22:51.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2025-12-15T05:03:06.000Z (6 months ago)
• Last Synced: 2025-12-17T09:45:02.121Z (6 months ago)
• Topics: algorithms, bioinformatics, cancer, computational-biology, evolution, phylogenetics, single-cell
• Language: Python
• Homepage: https://scphylo-tools.readthedocs.io
• Size: 22.5 MB
• Stars: 7
• Watchers: 2
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

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README

          
|Stars| |Compatible| |PyPI| |PyPiDownloads| |Contributions Welcome| |Build Status|

|Docs Status| |Pre-commit| |License| |Code Style|

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 `_.

.. 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

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    :target: https://github.com/faridrashidi/scphylo-tools/blob/master/CONTRIBUTING.rst

    :alt: Contributions Welcome

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    :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

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    :target: https://github.com/faridrashidi/scphylo-tools/blob/main/LICENSE

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