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@CollepardoLab Multiscale Chromatin Modelling

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    11 repositories

    • Russell_2026

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2026Jul 22, 2026

    • Nucleosome_Pulling

      Public
      Single nucleosome pulling package
      Python
      •0•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • Chromatin_MSM

      Public
      Structural sampling and Markov state model construction of chromatin
      Jupyter Notebook
      •1•0•0•0•Updated Jun 27, 2026Jun 27, 2026

    • Shimazoe_2026

      Public
      Source Code for the simulations of the paper 'Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells'
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • OpenCGChromatin

      Public
      GPU-accelerated chemically specific chromatin model
      Python
      •
      MIT License
      •2•4•1•0•Updated Feb 3, 2026Feb 3, 2026

    • Huertas_2025_Oct4

      Public
      Source Code for the paper 'Oct4 clusters promote DNA accessibility by enhancing chromatin plasticity'
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • MinimalCoacervates

      Public
      Scripts from our paper: Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • OpenMpipi

      Public
      Python
      •
      MIT License
      •5•9•0•0•Updated Jun 10, 2025Jun 10, 2025

    • NucleosomeLinker

      Public
      Source Code for the paper 'Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly'
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated May 6, 2025May 6, 2025

    • CollepardoLab_Chromatin_Model

      Public
      Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".
      C++
      •
      GNU General Public License v3.0
      •2•13•9•0•Updated Jun 17, 2022Jun 17, 2022

    • md_patchy_model

      Public
      Fortran
      •2•7•1•0•Updated Oct 16, 2020Oct 16, 2020
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