Chromosome polymer simulations and in silico capture experiments
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Oct 4, 2026 - Python
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loop-extrusion
Here are 9 public repositories matching this topic...
High-performance stochastic modeling of DNA loop extrusion interactions
bioinformatics cpp tad biology high-performance dna cpp17 hic loop-extrusion stochastic-model topologically-associated-domains
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Dec 22, 2025 - C++
StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning
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Oct 19, 2026 - Python
Loop extrusion module with LAMMPS
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Nov 15, 2022 - C++
Code to model active loop extrusion on chromatin using hybrid MD-MC.
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May 22, 2024 - C
LAMMPS code to simulate loop extrusion of DNA by SMC complexes
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Sep 4, 2026 - Python
Chromatin loop extrusion as a sequence model's routing operator: 36 runs vs attention, BiLSTM and a one-arm ablation, 8x length and 300-sequence tests, learned CTCF orientation.
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Oct 20, 2026 - Python
Analysis scripts and other code written during my time at Penn.
python bash bioinformatics rna-seq r simulation computational-biology chip-seq orca hic bash-scripting bash-tool single-cell-genomics hichip upenn polymer-simulation university-of-pennsylvania loop-extrusion
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Aug 12, 2025 - TeX
Scripts for running OpenMM polychrom-based coarse-grained polymer simulations of chromatin
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Jul 7, 2026 - Python
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