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This is a repo for codes to simulate trans-grabbing loop extrusion factors (developed by Andrea Bonato)
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Here you will find the c++ codes and LAMMPS scripts to run simulations of the topological relaxation of bead-spring polymers (which are initially knotted) by the action of a simulated TopoII protein.
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Python software for processing CRAC and CLIP type data. Compatible with Python 2 and 3.
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Analysis of poly-A selected RNA sequencing from human whole blood samples of COVID-19 patients.
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Statistical Experimental Design for Traveltime Tomography Problems
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Codes to run "superstructure" a modified version of DBSCAN. See https://rupress.org/jcb/article/220/5/e202010003/211893/Parameter-free-molecular-super-structures
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Codes to simulate condensins and loop extruders that can grab polymer segments in 3D. Developed by Andrea Bonato
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