This repository encompasses folders containing polymer simulations conducted for the project titled "Need for Speed: Loop Extrusion Velocity Shapes Chromosome Conformation and Morphology." It includes:
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"simulations": This folder houses the necessary files for running MD simulations of loop extrusion.
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"data"
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"analysis": Within this section, you'll find Jupyter notebooks responsible for generating contact maps, computing P(s), performing pile-up analysis, calculating peak scores, and more.
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"figures"