Metadata-Version: 2.1
Name: trisicell
Version: 0.0.12
Summary: UNKNOWN
Home-page: https://github.com/faridrashidi/trisicell
Author: Farid Rashidi
Author-email: farid.rsh@gmail.com
Maintainer: Farid Rashidi
Maintainer-email: farid.rsh@gmail.com
License: BSD
Download-URL: https://github.com/faridrashidi/trisicell
Project-URL: Documentation, https://trisicell.readthedocs.io/en/latest
Project-URL: Source Code, https://github.com/faridrashidi/trisicell
Keywords: tumor phylogeny,single cell,scalable,rna-seq,dna-seq
Platform: Linux
Platform: MacOSX
Classifier: License :: OSI Approved :: BSD License
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Framework :: Jupyter
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
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License-File: LICENSE
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|DOI| |Stars| |Compatible| |PyPI| |PyPiDownloads| |Contributions Welcome| |Build Status|
|Docs Status| |Pre-commit| |Code Score| |License| |Code Style|


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


.. image:: https://raw.githubusercontent.com/faridrashidi/trisicell/master/docs/source/_static/images/overview.png
   :target: https://trisicell.readthedocs.io
   :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.


Manuscript
----------
Please see our `preprint`_ on **bioRxiv** to learn more.


Support
-------
Feel free to submit an `issue <https://github.com/faridrashidi/trisicell/issues/new/choose>`_
or send us an `email <mailto:farid.rsh@gmail.com>`_.
Your help to improve Trisicell is highly appreciated.

Trisicell was developed in collaboration between the `Cancer Data Science Laboratory (CDSL) <https://ccr.cancer.gov/cancer-data-science-laboratory>`_ and the `Laboratory of Cancer Biology and Genetics (LCBG) <https://ccr.cancer.gov/laboratory-of-cancer-biology-and-genetics>`_ at the `National Cancer Institute (NCI) <https://www.cancer.gov>`_.


.. |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

.. |PyPiDownloads| image:: https://img.shields.io/pypi/dm/trisicell.svg?logo=docusign&logoColor=FFFFFF&style=flat-square&color=blue
    :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=0059b3&logo=handshake&logoColor=FFFFFF&style=flat-square
    :target: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.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/workflow/status/faridrashidi/trisicell/CI/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-enabled-brightgreen?logo=pre-commit&logoColor=white&style=flat-square
    :target: https://github.com/pre-commit/pre-commit
    :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


