Repositories list

• 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

  •6060 forks•243243 stars•4343 issues•1313 pull requests•Updated Aug 31, 2026Aug 31, 2026

• polychrom

  Public
  Chromosome polymer simulations and in silico capture experiments

  polymersimulationhi-c+ 3

  polymersimulationhi-cchromatinchromosomesloop-extrusion

  Python

  •

  MIT License

  •1818 forks•6464 stars•99 issues•00 pull requests•Updated Aug 9, 2026Aug 9, 2026

• bioframe

  Public
  Genomic interval operations on Pandas DataFrames

  pythonbioinformaticsgenomics+ 7

  pythonbioinformaticsgenomicsnumpypandasdataframesngs-analysisgenomic-rangesspatial-joingenomic-intervals

  Python

  •

  MIT License

  •3636 forks•195195 stars•3030 issues•44 pull requests•Updated Aug 3, 2026Aug 3, 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

  •33 forks•55 stars•88 issues•00 pull requests•Updated Aug 2, 2026Aug 2, 2026

• pairtools

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

  pythonbioinformaticsngs+ 4

  pythonbioinformaticsngshi-c3d-genomefile-formatterpairs-file

  Python

  •

  MIT License

  •3838 forks•138138 stars•4848 issues•55 pull requests•Updated Jul 29, 2026Jul 29, 2026

• polychrom-hoomd

  Public
  Python

  •

  MIT License

  •66 forks•1010 stars•22 issues•11 pull request•Updated Jun 9, 2026Jun 9, 2026

• polykit

  Public
  Python

  •

  MIT License

  •44 forks•99 stars•22 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• cooltools

  Public
  The tools for your .cool's

  Jupyter Notebook

  •

  MIT License

  •5656 forks•169169 stars•6161 issues•1010 pull requests•Updated Mar 19, 2026Mar 19, 2026

• .github

  Public
  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•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

  •88 forks•1111 stars•44 issues•33 pull requests•Updated Feb 10, 2025Feb 10, 2025

• open2c.github.io

  Public
  Welcome to the Open Chromosome Collective!

  Ruby

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 20, 2025Jan 20, 2025

• distiller-nf

  Public
  A modular Hi-C mapping pipeline

  pipelinenextflowhi-c

  pipelinenextflowhi-c

  Groovy

  •

  MIT License

  •2727 forks•105105 stars•6464 issues•44 pull requests•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

  •1212 forks•8282 stars•1111 issues•11 pull request•Updated Oct 31, 2024Oct 31, 2024

• assemblyinfo

  Public
  Genome assembly metadata

  Python

  •

  MIT License

  •11 fork•22 stars•00 issues•11 pull request•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

  •684684 forks•22 stars•22 issues•00 pull requests•Updated Jul 21, 2024Jul 21, 2024

• quaich

  Public template
  snakemake pipeline for Hi-C post-processing

  workflowsnakemakeanalysis+ 1

  workflowsnakemakeanalysishi-c

  Python

  •

  MIT License

  •66 forks•2222 stars•77 issues•00 pull requests•Updated Jun 27, 2024Jun 27, 2024

• gsoc

  Public
  Google Summer of Code - Open2C

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2024Mar 19, 2024

• open2c_examples

  Public
  Jupyter Notebook

  •77 forks•1818 stars•1111 issues•22 pull requests•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

  •22 forks•44 stars•22 issues•00 pull requests•Updated Feb 7, 2024Feb 7, 2024

• inspectro-nf

  Public
  Python

  •11 fork•77 stars•00 issues•00 pull requests•Updated Nov 23, 2023Nov 23, 2023

• bioframe-poster

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

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2023Apr 14, 2023

• inspectro

  Public
  Hi-C spectral analysis workflow

  Python

  •33 forks•88 stars•33 issues•00 pull requests•Updated Apr 13, 2023Apr 13, 2023

• pairtools-1

  Public
  CLI tools to process mapped Hi-C data

  Python

  •

  MIT License

  •3838 forks•11 star•00 issues•00 pull requests•Updated Sep 1, 2022Sep 1, 2022

• pairlib

  Public
  Read, write and analyse Hi-C pairs

  Python

  •

  MIT License

  •00 forks•33 stars•44 issues•00 pull requests•Updated Apr 4, 2022Apr 4, 2022

• MultiQC_TestData

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

  HTML

  •

  MIT License

  •166166 forks•00 stars•00 issues•00 pull requests•Updated Dec 19, 2021Dec 19, 2021

• cooler-binder

  Public
  Cooler demo using a Jupyter notebook Binder

  Jupyter Notebook

  •77 forks•2020 stars•22 issues•00 pull requests•Updated Sep 24, 2020Sep 24, 2020

• pyfilesplit

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 21, 2018Dec 21, 2018

• distiller-test-data

  Public
  Test data for distiller

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2018Jul 19, 2018