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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 Public

    A cool place to store your Hi-C

    Python 214 56

  2. cooltools Public

    The tools for your .cool's

    Jupyter Notebook 147 51

  3. pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 108 33

  4. bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 182 36

  5. distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 92 25

  6. polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 47 16

Repositories

Showing 10 of 28 repositories
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 182 MIT 36 28 6 Updated Mar 17, 2025
  • cooler Public

    A cool place to store your Hi-C

    Python 214 BSD-3-Clause 56 35 (1 issue needs help) 8 Updated Mar 17, 2025
  • .github Public
    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.

    Cython 10 6 3 3 Updated Feb 10, 2025
  • distiller-sm Public

    a Snakemake version of distiller - the Open2C Hi-C mapping workflow

    Python 4 MIT 3 8 0 Updated Jan 31, 2025
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 108 MIT 33 42 (2 issues need help) 6 Updated Jan 31, 2025
  • polychrom-hoomd Public
    Python 7 MIT 4 0 0 Updated Jan 29, 2025
  • open2c.github.io Public

    Welcome to the Open Chromosome Collective!

    Ruby 2 2 0 0 Updated Jan 20, 2025
  • distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 92 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.

    Python 79 MIT 12 12 0 Updated Oct 31, 2024
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