trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

https://github.com/faridrashidi/trisicell

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Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

README.rst

|DOI| |Stars| |Compatible| |PyPI| |PyPiDownloads| |Contributions Welcome| |Build Status|
|Docs Status| |Pre-commit| |Codecov| |License| |Code Style|


Trisicell - |subst|
===================


.. image:: https://raw.githubusercontent.com/faridrashidi/trisicell/master/docs/source/_static/images/overview.png
   :target: https://github.com/faridrashidi/trisicell
   :alt: overview
   :align: center


Trisicell (**Tri**\ ple-toolkit for **si**\ ngle-\ **cell** intratumor
heterogeneity inference), pronounced as "tricycle", is a new computational
toolkit for scalable intratumor heterogeneity inference and evaluation from
single-cell RNA, as well as single-cell genome or exome, sequencing data.
Trisicell utilizes expressed SNVs and Indels to infer evolutionary
relationships between genomic alterations and the cells that harbor them.


Support
-------
Feel free to submit an `issue `_.
Your help to improve Trisicell is highly appreciated.

Trisicell was developed in collaboration between the `Cancer Data Science Laboratory (CDSL) `_ and the `Laboratory of Cancer Biology and Genetics (LCBG) `_ at the `National Cancer Institute (NCI) `_.


.. |subst| replace:: Scalable intratumor heterogeneity inference and validation
                    from single-cell data

.. |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/trisicell?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue
    :target: https://pypi.org/project/trisicell
    :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%2Ftrisicell
    :target: https://pepy.tech/project/trisicell
    :alt: PyPyDownloads

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    :target: https://pepy.tech/project/trisicell
    :alt: PyPiDownloads

.. |Stars| image:: https://img.shields.io/github/stars/faridrashidi/trisicell?logo=GitHub&color=yellow&style=flat-square
    :target: https://github.com/faridrashidi/trisicell
    :alt: Stars

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

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

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

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

.. |Pre-commit| image:: https://img.shields.io/badge/pre--commit.ci-passing-brightgreen?logo=pre-commit&logoColor=white&style=flat-square
    :target: https://results.pre-commit.ci/latest/github/faridrashidi/trisicell/master
    :alt: Pre-commit

.. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg?logo=visualstudiocode&logoColor=FFFFFF&style=flat-square
    :target: https://github.com/python/black
    :alt: Code Style

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

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

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


.. _preprint: https://doi.org/10.1101/2021.03.26.437185

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
title: "Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity"
message: "To cite Trisicell in publications, please cite it as below:"
type: "article"
authors:
  - family-names: "Rashidi Mehrabadi"
    given-names: "Farid"
    orcid: "https://orcid.org/0000-0003-4103-4904"
doi: "10.1101/2021.03.26.437185"
url: "https://doi.org/10.1101/2021.03.26.437185"
journal: "bioRxiv"
year: "2021"

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