Polymer simulations with loop extrusion and transcription

The code in this repository was used for the paper 'Transcription shapes 3D chromatin organization by interacting with loop-extrusion', available at https://www.biorxiv.org/content/10.1101/2022.01.07.475367v2

Dependencies

https://github.com/mirnylab/openmm-polymer-legacy

https://github.com/open2c/cooler

https://github.com/open2c/bioframe

Setup

Run setup.py to compile the cython (.pyx) files