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meyer-lab / tHMM

A general Python framework for using hidden Markov models on binary trees or cell lineage trees.
https://asmlab.org
MIT License
9 stars 1 forks source link
bioengineering cell-biology drug-response heterogeneity inference

readme

==== tHMM

.. image:: https://codecov.io/gh/meyer-lab/tHMM/branch/master/graph/badge.svg :target: https://codecov.io/gh/meyer-lab/tHMM

.. image:: https://readthedocs.org/projects/tHMM/badge/?version=latest :target: https://lineage-growth.readthedocs.io/

tHMM is a Python3 package for clustering, visualizing, and analyzing data in the form of lineage trees. This work is now published in Communications Biology https://www.nature.com/articles/s42003-022-04208-9

Install

.. code-block:: console

$ git clone https://github.com/meyer-lab/tHMM.git

It takes a few seconds to clone the repository.

Software Requirements

This package is supported on macOS and Linux systems.

Python dependencies



``tHMM`` requires ``virtualenv``. All other required packages can then be installed using ``make venv`` to establish a virtual environment. 
The Python packages that will be installed are listed in pyproject.toml, and can be directly installed using ``poetry install``.

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

Please find the documentation at https://thmm.readthedocs.io.

License
-------

This project is covered under the MIT License.