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@open2c

Open Chromosome Collective

README.md

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  1. cooler cooler Public

    A cool place to store your Hi-C

    Python 211 53

  2. cooltools cooltools Public

    The tools for your .cool's

    Jupyter Notebook 143 51

  3. pairtools pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    Python 106 32

  4. bioframe bioframe Public

    Genomic interval operations on Pandas DataFrames

    Python 177 30

  5. distiller-nf distiller-nf Public

    A modular Hi-C mapping pipeline

    Groovy 88 25

  6. polychrom polychrom Public

    Chromosome polymer simulations and in silico capture experiments

    Python 47 16

Repositories

Showing 10 of 28 repositories
  • pairtools Public

    Extract 3D contacts (.pairs) from sequencing alignments

    open2c/pairtools’s past year of commit activity
    Python 106 MIT 32 41 (2 issues need help) 5 Updated Jan 20, 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
  • bioframe Public

    Genomic interval operations on Pandas DataFrames

    open2c/bioframe’s past year of commit activity
    Python 177 MIT 30 28 2 Updated Jan 20, 2025
  • cooler Public

    A cool place to store your Hi-C

    open2c/cooler’s past year of commit activity
    Python 211 BSD-3-Clause 53 32 (1 issue needs help) 3 Updated Jan 20, 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 Jan 16, 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 4 MIT 3 8 0 Updated Dec 19, 2024
  • polychrom-hoomd Public
    open2c/polychrom-hoomd’s past year of commit activity
    Python 7 MIT 4 0 0 Updated Dec 16, 2024
  • distiller-nf Public

    A modular Hi-C mapping pipeline

    open2c/distiller-nf’s past year of commit activity
    Groovy 88 MIT 25 64 (2 issues need help) 3 Updated Dec 5, 2024
  • .github Public
    open2c/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Nov 7, 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 78 MIT 12 8 0 Updated Oct 31, 2024
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