mirnylab/moving-barriers-paper

Simulation and analysis codes used in Banigan*, Tang*, van den Berg* et al. Transcription shapes 3D chromatin organization by interacting with loop-extruding cohesin complexes, bioRxiv (2021)

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