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A general Python framework for using hidden Markov models on binary trees or cell lineage trees.

Home Page: https://asmlab.org

License: MIT License

Makefile 0.22% Python 99.49% Batchfile 0.29%
inference bioengineering cell-biology heterogeneity drug-response

thmm's Introduction

tHMM

https://readthedocs.org/projects/tHMM/badge/?version=latest

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

$ 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.

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