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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 243 61

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 170 56

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 138 39

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 195 36

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 105 27

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 65 19

Repositories

Showing 10 of 28 repositories
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe's past year of commit activity
    Python 195 MIT 36 30 4 Updated Sep 7, 2026
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler's past year of commit activity
    Python 243 BSD-3-Clause 61 44 (1 issue needs help) 14 Updated Sep 7, 2026
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom's past year of commit activity
    Python 65 MIT 19 9 (1 issue needs help) 0 Updated Aug 9, 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 Aug 2, 2026
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools's past year of commit activity
    Python 138 MIT 39 48 (2 issues need help) 5 Updated Jul 29, 2026
  • polychrom-hoomd Public
    open2c/polychrom-hoomd's past year of commit activity
    Python 10 MIT 6 2 1 Updated Jun 9, 2026
  • polykit Public
    open2c/polykit's past year of commit activity
    Python 9 MIT 4 2 0 Updated Jun 9, 2026
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools's past year of commit activity
    Jupyter Notebook 170 MIT 56 61 10 Updated Mar 19, 2026
  • .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 4 3 Updated Feb 10, 2025
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