semvec/pypi-packages huggingface dataset:
comut 0.0.3
A Python library for creating comutation plots to visualize genomic and phenotypic information
License: MIT
Requires Python: >=3.6

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

![melanoma_comut](https://raw.githubusercontent.com/vanallenlab/comut/master/examples/images/melanoma_comut.png)


## Installation

CoMut 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](https://colab.research.google.com/github/vanallenlab/comut/blob/master/examples/quickstart.ipynb) where you can simply upload a [MAF](https://software.broadinstitute.org/software/igv/MutationAnnotationFormat) file and run the notebook to make a basic comut. This file is also available as a [jupyter notebook](https://github.com/vanallenlab/comut/blob/master/examples/quickstart.ipynb) for local use. 

## Citation 

CoMut is now available on biorxiv https://www.biorxiv.org/content/10.1101/2020.03.18.997361v1. If you use CoMut in a paper, please cite:
> Crowdis, J., He, M.X., Reardon, B., Van Allen, E.M. (2020). CoMut: Visualizing integrated molecular information with comutation plots. bioRxiv doi: 10.1101/2020.03.18.997361v1

## Documentation

There is also a [Documentation notebook](https://github.com/vanallenlab/comut/blob/master/examples/documentation.ipynb) that provides documentation for CoMut. It describes the fundamentals of creating comuts 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](https://github.com/vanallenlab/comut/issues)

## 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