chromosome-network-modeling

This repository contains the scripts needed to reproduce the analysis published in Parental and stochastic skewing of X-chromosome inactivation predicts phenotypic penetrance of fragile X syndrome (citation link to come)

To reproduce this work:

1. Clone this repository

git clone https://github.com/AllenInstitute/chromosome-network-modeling.git

2. Install requirements (example uses virtualenv, one could also use conda or other enviroment manager):
   • Install virtualenv if necessary:

   python3 -m pip install --user virtualenv
   

   • Create a new environment

   cd chromosome-network-modeling
   python3 -m venv env
   

   • Activate and install requirements

   source env/bin/activate
   pip install -r requirements.txt
   

3. To reproduce the analysis, run the following script:

python3 run_test_distance_sample.py