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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 248 62

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 172 57

  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 196 38

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 106 27

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 68 21

Repositories

Showing 10 of 28 repositories
  • cooltools Public

    The tools for your .cool's

    open2c/cooltools's past year of commit activity
    Jupyter Notebook 172 MIT 57 62 10 Updated Oct 30, 2026
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler's past year of commit activity
    Python 248 BSD-3-Clause 62 15 (1 issue needs help) 1 Updated Oct 30, 2026
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe's past year of commit activity
    Python 196 MIT 38 30 6 Updated Oct 5, 2026
  • polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    open2c/polychrom's past year of commit activity
    Python 68 MIT 21 9 (1 issue needs help) 0 Updated Oct 4, 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 6 MIT 4 8 0 Updated Sep 29, 2026
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools's past year of commit activity
    Python 138 MIT 39 49 (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
  • .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