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CoMut

CoMut is a Python library for creating comutation plots to visualize genomic and phenotypic information.

Installation

CoMut is available on pypi here and can be installed via pip

pip install comut

Colab Quickstart

For those who do not want to install Python or other packages, there is a Google Colab notebook where you can simply upload a MAF file and run the notebook to make a basic comutation plot. This file is also available as a jupyter notebook for local use.

Citation

CoMut is now published here - https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btaa554/5851837. If you use CoMut in a paper, please cite:

Crowdis, J., He, M.X., Reardon, B. & Van Allen, E. M. CoMut: Visualizing integrated molecular information with comutation plots. Bioinformatics (2020). doi:10.1093/bioinformatics/btaa554

Documentation

There is also a Documentation notebook that provides documentation for CoMut. It describes the fundamentals of creating comutation plots and provides the code used to generate the comut above.

Development

If you would like to report a bug or request a feature, please do so using the issues page

Dependencies

CoMut runs on python 3.6 or later. CoMut requires the following packages as dependencies (they will be installed along with CoMut if using pip)

numpy>=1.18.1
pandas>=0.25.3
palettable>=3.3.0
matplotlib>=3.3.1

Versions

0.0.3 - No code is changed, description updated for public release
0.0.2 - Introduce compatability for Python 3.6
0.0.1 - Initial release