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@open2c

Open Chromosome Collective

README.md

Welcome to Open2C!

Open2C is a community that develops and maintains open-source tools for 3D chromosome biology and genomic data science, primarily in Python.

Here's how to get started:

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  1. cooler cooler Public

    A cool place to store your Hi-C

    Python 230 59

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 158 54

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 123 36

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 185 35

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 100 27

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 53 17

Repositories

Showing 10 of 28 repositories
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 230 BSD-3-Clause 59 40 (1 issue needs help) 10 Updated Jan 12, 2026
  • distiller-sm Public

    a Snakemake version of distiller - the Open2C Hi-C mapping workflow

    open2c/distiller-sm’s past year of commit activity
    Python 5 MIT 3 8 0 Updated Jan 12, 2026
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 123 MIT 36 45 (2 issues need help) 6 Updated Jan 9, 2026
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 185 MIT 35 29 2 Updated Jan 5, 2026
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom’s past year of commit activity
    Python 53 MIT 17 9 (1 issue needs help) 1 Updated Nov 11, 2025
  • polykit Public
    open2c/polykit’s past year of commit activity
    Python 9 MIT 4 2 1 Updated Oct 22, 2025
  • polychrom-hoomd Public
    open2c/polychrom-hoomd’s past year of commit activity
    Python 9 MIT 5 0 0 Updated Oct 22, 2025
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools’s past year of commit activity
    Jupyter Notebook 158 MIT 54 60 8 Updated Jul 7, 2025
  • .github Public
    open2c/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Feb 10, 2025
  • looplib Public

    A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.

    open2c/looplib’s past year of commit activity
    Cython 11 8 3 3 Updated Feb 10, 2025
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