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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 236 60

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 164 55

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 130 36

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 191 35

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 102 27

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 57 17

Repositories

Showing 10 of 28 repositories
  • 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 1 Updated Apr 8, 2026
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 191 MIT 35 29 2 Updated Apr 6, 2026
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 236 BSD-3-Clause 60 41 (1 issue needs help) 10 Updated Apr 6, 2026
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools’s past year of commit activity
    Jupyter Notebook 164 MIT 55 61 9 Updated Mar 19, 2026
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom’s past year of commit activity
    Python 57 MIT 17 9 (1 issue needs help) 1 Updated Feb 18, 2026
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 130 MIT 36 48 (2 issues need help) 7 Updated Feb 3, 2026
  • 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
  • .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
View all repositories

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