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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 224 58

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 153 52

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 116 36

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 184 34

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 98 26

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 51 17

Repositories

Showing 10 of 28 repositories
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 184 MIT 34 29 1 Updated Sep 5, 2025
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 224 BSD-3-Clause 58 38 (1 issue needs help) 10 Updated Sep 5, 2025
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 116 MIT 36 42 (2 issues need help) 7 Updated Aug 20, 2025
  • polykit Public
    open2c/polykit’s past year of commit activity
    Python 6 MIT 3 2 0 Updated Aug 13, 2025
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom’s past year of commit activity
    Python 51 MIT 17 9 (1 issue needs help) 0 Updated Jul 25, 2025
  • polychrom-hoomd Public
    open2c/polychrom-hoomd’s past year of commit activity
    Python 7 MIT 4 0 0 Updated Jul 22, 2025
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools’s past year of commit activity
    Jupyter Notebook 153 MIT 52 56 8 Updated Jul 7, 2025
  • 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 Jun 25, 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 10 7 3 3 Updated Feb 10, 2025
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