Clin-MSI

Source code for MSI Detection in tumor samples.

Installation

pip

pip install clin-msi

conda from Bioconda channel

conda install -c bioconda clin-msi

How to use clin-msi?

Usage:

clin-msi <command> [options]

Key Commands:

• train

  Train your model by supplying BAM files with their associated MSI status

• predict

  Predict the MSI status of a BAM by comparing it to your trained model

Development

The package is managed using

Install Poetry

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
source $HOME/.poetry/env

Install projects dependencies

poetry install -v