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@CollepardoLab

Multiscale Chromatin Modelling

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  1. CollepardoLab_Chromatin_Model CollepardoLab_Chromatin_Model Public

    Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".

    C++ 13 2

  2. OpenMpipi OpenMpipi Public

    Python 10 5

  3. md_patchy_model md_patchy_model Public

    Fortran 7 2

  4. OpenCGChromatin OpenCGChromatin Public

    GPU-accelerated chemically specific chromatin model

    Python 4 2

  5. NucleosomeLinker NucleosomeLinker Public

    Source Code for the paper 'Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly'

    Python 3

  6. MinimalCoacervates MinimalCoacervates Public

    Scripts from our paper: Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry

    Python

Repositories

Showing 10 of 11 repositories
  • Chromatin_MSM Public

    Structural sampling and Markov state model construction of chromatin

    CollepardoLab/Chromatin_MSM's past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Oct 21, 2026
  • Nucleosome_Pulling Public

    Single nucleosome pulling package

    CollepardoLab/Nucleosome_Pulling's past year of commit activity
    Python 0 0 0 0 Updated Oct 1, 2026
  • Russell_2026 Public
    CollepardoLab/Russell_2026's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Aug 3, 2026
  • OpenCGChromatin Public

    GPU-accelerated chemically specific chromatin model

    CollepardoLab/OpenCGChromatin's past year of commit activity
    Python 4 MIT 2 1 0 Updated Aug 3, 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'

    CollepardoLab/Shimazoe_2026's past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Mar 2, 2026
  • Huertas_2025_Oct4 Public

    Source Code for the paper 'Oct4 clusters promote DNA accessibility by enhancing chromatin plasticity'

    CollepardoLab/Huertas_2025_Oct4's past year of commit activity
    0 AGPL-3.0 0 0 0 Updated Jan 7, 2026
  • MinimalCoacervates Public

    Scripts from our paper: Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry

    CollepardoLab/MinimalCoacervates's past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Sep 23, 2025
  • OpenMpipi Public
    CollepardoLab/OpenMpipi's past year of commit activity
    Python 10 MIT 5 0 0 Updated Jun 10, 2025
  • NucleosomeLinker Public

    Source Code for the paper 'Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly'

    CollepardoLab/NucleosomeLinker's past year of commit activity
    Python 3 GPL-3.0 0 0 0 Updated May 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".

    CollepardoLab/CollepardoLab_Chromatin_Model's past year of commit activity
    C++ 13 GPL-3.0 2 9 0 Updated Jun 17, 2022
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