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@mirnylab

mirnylab

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  1. Open2C Public

    Community software repositories (cooler, cooltools, pairtools, distiller, polychrom, bioframe, and others) now live at https://github.com/open2c

    1

  2. 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 5

  3. one_sided_extrusion Public

    Codes relevant for "Chromosome organization by one-sided and two-sided loop extrusion"

    Jupyter Notebook 7 3

  4. nglutils Public

    Utility module for using nglview to visualize stuff

    Python 2 1

Repositories

Showing 10 of 20 repositories
  • lefs-cython Public

    A cython-based LEF translocator for fast 1D extrusion simulations

    Python 0 MIT 0 0 1 Updated Jan 23, 2025
  • microcompartments Public

    Polymer simulations of compartments and extrusion modeling the mitosis-to-G1 transition

    Python 0 MIT 0 0 0 Updated Jan 8, 2025
  • dendritic_cells Public

    Code for the Hi-C data analysis in the dendritic cells project.

    Jupyter Notebook 0 MIT 0 0 0 Updated Sep 23, 2024
  • GenomeArchitectureAndFunction2024 Public

    Materials for the workshop at Genome Architecture and Function 2024 Workshop

    Jupyter Notebook 2 MIT 0 0 0 Updated Jul 8, 2024
  • GenomeArchitectureAndFunction2023 Public

    Materials for the workshop at Genome Architecture and Function 2023 Workshop

    Jupyter Notebook 5 MIT 0 0 0 Updated Jun 4, 2023
  • chicken2.0_paper Public

    Repository for analysis code related to Chicken2.0

    Jupyter Notebook 1 0 0 0 Updated May 18, 2023
  • heterochromatin-paper Public
    Jupyter Notebook 5 MIT 0 0 0 Updated Jan 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 cohesin complexes, bioRxiv (2021)

    Python 6 MIT 1 1 0 Updated Jun 22, 2022
  • MCMs-as-random-barriers-to-loop-extrusion-paper Public
    Jupyter Notebook 3 MIT 0 0 0 Updated Jan 31, 2022
  • one_sided_extrusion Public

    Codes relevant for "Chromosome organization by one-sided and two-sided loop extrusion"

    Jupyter Notebook 7 MIT 3 0 0 Updated Jul 16, 2021
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