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    21 repositories

    • dendritic_cells

      Public
      Code for the Hi-C data analysis in the dendritic cells project.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • lefs-cython

      Public
      A cython-based LEF translocator for fast 1D extrusion simulations
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 25, 2025Oct 25, 2025

    • microcompartments

      Public
      Polymer simulations of compartments and extrusion modeling the mitosis-to-G1 transition
      Python
      •
      MIT License
      •2•2•0•0•Updated Aug 27, 2025Aug 27, 2025

    • Hi-C_Workshop

      Public
      Materials for the workshop at Genome Architecture and Function 2024 Workshop
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jun 3, 2025Jun 3, 2025

    • bombyx2024

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • GenomeArchitectureAndFunction2023

      Public
      Materials for the workshop at Genome Architecture and Function 2023 Workshop
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Jun 4, 2023Jun 4, 2023

    • chicken2.0_paper

      Public
      Repository for analysis code related to Chicken2.0
      Jupyter Notebook
      •0•1•0•0•Updated May 18, 2023May 18, 2023

    • heterochromatin-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Jan 13, 2023Jan 13, 2023

    • moving-barriers-paper

      Public
      Simulation and analysis codes used in Banigan*, Tang*, van den Berg* et al. Transcription shapes 3D chromatin organization by interacting with loop-extruding co…
      Python
      •
      MIT License
      •1•6•1•0•Updated Jun 22, 2022Jun 22, 2022

    • MCMs-as-random-barriers-to-loop-extrusion-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •1•4•0•0•Updated Jan 31, 2022Jan 31, 2022

    • one_sided_extrusion

      Public
      Codes relevant for "Chromosome organization by one-sided and two-sided loop extrusion"
      Jupyter Notebook
      •
      MIT License
      •3•8•0•0•Updated Jul 16, 2021Jul 16, 2021

    • nglutils

      Public
      Utility module for using nglview to visualize stuff
      Python
      •
      MIT License
      •1•2•2•0•Updated Jun 21, 2021Jun 21, 2021

    • TMB_analysis

      Public
      R code and data for "Limited evidence of tumour mutational burden as a biomarker of response to immunotherapy", C Gurjao et al., 2020
      R
      •0•5•0•0•Updated Nov 17, 2020Nov 17, 2020

    • Open2C

      Public
      Community software repositories (cooler, cooltools, pairtools, distiller, polychrom, bioframe, and others) now live at https://github.com/open2c
      0•2•0•0•Updated Nov 12, 2020Nov 12, 2020

    • cont3d

      Public
      Utilities for working with 3-point contact matrices
      Python
      •2•2•0•0•Updated Apr 20, 2020Apr 20, 2020

    • hiclib-legacy

      Public
      A legacy repository. Was replaced by distiller, cooler, and cooltools.
      Python
      •
      MIT License
      •7•21•0•0•Updated Mar 4, 2020Mar 4, 2020

    • mirnylib-legacy

      Public
      A legacy repository. Useful functionality was ported to cooltools.lib.numutils.
      Python
      •
      MIT License
      •1•3•2•0•Updated Feb 17, 2020Feb 17, 2020

    • openmm-polymer-legacy

      Public
      A legacy repository. Was replaced by polychrom.
      HTML
      •
      MIT License
      •1•1•0•0•Updated Feb 17, 2020Feb 17, 2020

    • GSG_mitotic_models_2018

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 10, 2019May 10, 2019

    • pdSim

      Public
      Gillespie simulations of advantageous drivers & deleterious passengers in cancer
      cythonpython3population-genetics
      cythonpython3population-geneticsgillespie-algorithmcancer-evolution
      C
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2019Feb 4, 2019

    • pairsamtools

      Public
      a legacy repo to avoid breaking existing pipelines
      Python
      •
      MIT License
      •1•1•0•0•Updated Jul 18, 2018Jul 18, 2018
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