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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 215 56

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 150 51

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 110 33

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 183 37

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 94 25

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 48 16

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 4 MIT 3 8 0 Updated Apr 4, 2025
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 183 MIT 37 28 6 Updated Mar 24, 2025
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 215 BSD-3-Clause 56 36 (1 issue needs help) 8 Updated Mar 24, 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
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 110 MIT 33 43 (2 issues need help) 6 Updated Jan 31, 2025
  • polychrom-hoomd Public
    open2c/polychrom-hoomd’s past year of commit activity
    Python 7 MIT 4 0 0 Updated Jan 29, 2025
  • open2c.github.io Public

    Welcome to the Open Chromosome Collective!

    open2c/open2c.github.io’s past year of commit activity
    Ruby 2 2 0 0 Updated Jan 20, 2025
  • distiller-nf Public

    A modular Hi-C mapping pipeline

    open2c/distiller-nf’s past year of commit activity
    Groovy 94 MIT 25 64 (2 issues need help) 3 Updated Dec 5, 2024
  • coolpuppy Public

    A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

    open2c/coolpuppy’s past year of commit activity
    Python 79 MIT 12 12 0 Updated Oct 31, 2024
View all repositories

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