Repositories list

• cooltools

  Public
  The tools for your .cool's

  Jupyter Notebook

  •

  MIT License

  •55•162•60•9•Updated Mar 19, 2026Mar 19, 2026

• distiller-sm

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

  bioinformaticssnakemakebioinformatics-pipeline+ 4

  bioinformaticssnakemakebioinformatics-pipelinehi-chicsnakemake-workflowsnakemake-pipeline

  Python

  •

  MIT License

  •3•5•8•0•Updated Mar 18, 2026Mar 18, 2026

• cooler

  Public
  A cool place to store your Hi-C

  pythonbioinformaticsgenomics+ 9

  pythonbioinformaticsgenomicsngsfile-formatcontact-matrixhdf5sparsehi-ccooler+ 2

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •60•231•41•10•Updated Mar 16, 2026Mar 16, 2026

• bioframe

  Public
  Genomic interval operations on Pandas DataFrames

  pythonbioinformaticsgenomics+ 7

  pythonbioinformaticsgenomicsnumpypandasdataframesngs-analysisgenomic-rangesspatial-joingenomic-intervals

  Python

  •

  MIT License

  •35•191•29•2•Updated Mar 2, 2026Mar 2, 2026

• polychrom

  Public
  Chromosome polymer simulations and in silico capture experiments

  polymersimulationhi-c+ 3

  polymersimulationhi-cchromatinchromosomesloop-extrusion

  Python

  •

  MIT License

  •17•56•9•1•Updated Feb 18, 2026Feb 18, 2026

• pairtools

  Public
  Extract 3D contacts (.pairs) from sequencing alignments

  pythonbioinformaticsngs+ 4

  pythonbioinformaticsngshi-c3d-genomefile-formatterpairs-file

  Python

  •

  MIT License

  •36•128•48•7•Updated Feb 3, 2026Feb 3, 2026

• polykit

  Public
  Python

  •

  MIT License

  •4•9•2•1•Updated Oct 22, 2025Oct 22, 2025

• polychrom-hoomd

  Public
  Python

  •

  MIT License

  •5•9•0•0•Updated Oct 22, 2025Oct 22, 2025

• .github

  Public
  MIT License

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• looplib

  Public
  A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.

  Cython

  •8•11•3•3•Updated Feb 10, 2025Feb 10, 2025

• open2c.github.io

  Public
  Welcome to the Open Chromosome Collective!

  Ruby

  •1•2•0•0•Updated Jan 20, 2025Jan 20, 2025

• distiller-nf

  Public
  A modular Hi-C mapping pipeline

  pipelinenextflowhi-c

  pipelinenextflowhi-c

  Groovy

  •

  MIT License

  •27•101•64•3•Updated Dec 5, 2024Dec 5, 2024

• coolpuppy

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

  pythonbioinformaticsgenomics+ 4

  pythonbioinformaticsgenomicscontact-matrixhi-csparse-matrixpileup

  Python

  •

  MIT License

  •13•81•10•1•Updated Oct 31, 2024Oct 31, 2024

• assemblyinfo

  Public
  Genome assembly metadata

  Python

  •

  MIT License

  •1•2•0•1•Updated Aug 12, 2024Aug 12, 2024

• MultiQC

  Public
  Aggregate results from bioinformatics analyses across many samples into a single report.

  JavaScript

  •

  GNU General Public License v3.0

  •657•2•2•0•Updated Jul 21, 2024Jul 21, 2024

• quaich

  Public template
  snakemake pipeline for Hi-C post-processing

  workflowsnakemakeanalysis+ 1

  workflowsnakemakeanalysishi-c

  Python

  •

  MIT License

  •6•22•7•0•Updated Jun 27, 2024Jun 27, 2024

• gsoc

  Public
  Google Summer of Code - Open2C

  0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

• open2c_examples

  Public
  Jupyter Notebook

  •8•18•11•2•Updated Mar 12, 2024Mar 12, 2024

• open2c_vignettes

  Public
  A collection of notebooks and gists demonstrating novel applications of open2c ecosystem of tools

  Jupyter Notebook

  •2•4•2•0•Updated Feb 7, 2024Feb 7, 2024

• inspectro-nf

  Public
  Python

  •1•7•0•0•Updated Nov 23, 2023Nov 23, 2023

• bioframe-poster

  Public
  https://open2c.github.io/bioframe-poster

  Jupyter Notebook

  •0•0•0•0•Updated Apr 14, 2023Apr 14, 2023

• inspectro

  Public
  Hi-C spectral analysis workflow

  Python

  •3•8•3•0•Updated Apr 13, 2023Apr 13, 2023

• pairtools-1

  Public
  CLI tools to process mapped Hi-C data

  Python

  •

  MIT License

  •36•1•0•0•Updated Sep 1, 2022Sep 1, 2022

• pairlib

  Public
  Read, write and analyse Hi-C pairs

  Python

  •

  MIT License

  •0•3•4•0•Updated Apr 4, 2022Apr 4, 2022

• MultiQC_TestData

  Public
  Test data for MultiQC. See https://github.com/ewels/MultiQC

  HTML

  •

  MIT License

  •157•0•0•0•Updated Dec 19, 2021Dec 19, 2021

• cooler-binder

  Public
  Cooler demo using a Jupyter notebook Binder

  Jupyter Notebook

  •7•18•2•0•Updated Sep 24, 2020Sep 24, 2020

• pyfilesplit

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 21, 2018Dec 21, 2018

• distiller-test-data

  Public
  Test data for distiller

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jul 19, 2018Jul 19, 2018