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README.md

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# LoopExtrusion
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A tool to simulate chromatin loop extrusion with LAMMPS and estimate loop state proportions from simulations (closed vs extrusion vs open)
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A tool to simulate chromatin loop extrusion with LAMMPS and estimate loop state proportions from simulations (closed vs extruding vs open)
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This repository contains three directories:
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- **simulations** used to simulate a polymer with or without loop extrusion.
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- **simulated_data_subsample** contains a few polymer simulations with and without loop extrusion.
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- **Anchor-anchor_analysis** used to analyze simulated loop anchor coordinates to estimate loop state proportions (closed vs extrusion vs open) from simulated static imaging.
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- **Anchor-anchor_analysis** used to analyze simulated loop anchor coordinates to estimate loop state proportions (closed vs extruding vs open) from simulated static imaging.
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## Simulations

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