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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 220 56

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 154 52

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 113 33

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 183 34

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 97 26

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 51 16

Repositories

Showing 10 of 28 repositories
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 183 MIT 34 29 2 Updated Jul 7, 2025
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 220 BSD-3-Clause 56 39 (1 issue needs help) 8 Updated Jul 7, 2025
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools’s past year of commit activity
    Jupyter Notebook 154 MIT 52 56 8 Updated Jul 7, 2025
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 113 MIT 33 43 (2 issues need help) 6 Updated Jun 27, 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
  • polychrom-hoomd Public
    open2c/polychrom-hoomd’s past year of commit activity
    Python 7 MIT 4 0 0 Updated Jun 11, 2025
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom’s past year of commit activity
    Python 51 MIT 16 9 (1 issue needs help) 0 Updated Apr 16, 2025
  • polykit Public
    open2c/polykit’s past year of commit activity
    Python 6 MIT 3 1 0 Updated Apr 16, 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 6 3 3 Updated Feb 10, 2025
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