https://github.com/open2c/cooler

A cool place to store your Hi-C

3d-genome bioinformatics chromatin contact-matrix cooler file-format genomics hdf5 hi-c ngs python sparse

Last synced: 15 May 2025

https://github.com/open2c/bioframe

Genomic interval operations on Pandas DataFrames

bioinformatics dataframes genomic-intervals genomic-ranges genomics ngs-analysis numpy pandas python spatial-join

Last synced: 06 Oct 2025

https://github.com/open2c/cooltools

The tools for your .cool's

Last synced: 24 Apr 2025

https://github.com/open2c/pairtools

Extract 3D contacts (.pairs) from sequencing alignments

3d-genome bioinformatics file-formatter hi-c ngs pairs-file python

Last synced: 24 Apr 2025

https://github.com/open2c/distiller-nf

A modular Hi-C mapping pipeline

hi-c nextflow pipeline

Last synced: 09 Jul 2025

https://github.com/open2c/coolpuppy

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

bioinformatics contact-matrix genomics hi-c pileup python sparse-matrix

Last synced: 17 Jul 2025

https://github.com/open2c/polychrom

Chromosome polymer simulations and in silico capture experiments

chromatin chromosomes hi-c loop-extrusion polymer simulation

Last synced: 24 Apr 2025

https://github.com/open2c/quaich

snakemake pipeline for Hi-C post-processing

analysis hi-c snakemake workflow

Last synced: 24 Apr 2025

https://github.com/open2c/cooler-binder

Cooler demo using a Jupyter notebook Binder

Last synced: 24 Apr 2025

https://github.com/open2c/open2c_examples

Last synced: 24 Apr 2025

https://github.com/open2c/looplib

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

Last synced: 14 Feb 2026

https://github.com/open2c/inspectro

Hi-C spectral analysis workflow

Last synced: 27 Feb 2026

https://github.com/open2c/inspectro-nf

Last synced: 24 Apr 2025

https://github.com/open2c/polychrom-hoomd

Last synced: 24 Apr 2025

https://github.com/open2c/polykit

Last synced: 25 Feb 2026

https://github.com/open2c/distiller-sm

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

bioinformatics bioinformatics-pipeline hi-c hic snakemake snakemake-pipeline snakemake-workflow

Last synced: 16 Jul 2025

https://github.com/open2c/open2c_vignettes

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

Last synced: 24 Apr 2025

https://github.com/open2c/pairlib

Read, write and analyse Hi-C pairs

Last synced: 24 Apr 2025

https://github.com/open2c/assemblyinfo

Genome assembly metadata

Last synced: 12 Oct 2025

https://github.com/open2c/open2c.github.io

Welcome to the Open Chromosome Collective!

Last synced: 31 Jul 2025

https://github.com/open2c/pyfilesplit

Last synced: 24 Apr 2025

https://github.com/open2c/distiller-test-data

Test data for distiller

Last synced: 24 Apr 2025

https://github.com/open2c/gsoc

Google Summer of Code - Open2C

Last synced: 23 Jan 2026

https://github.com/open2c/bioframe-poster

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

Last synced: 16 Jun 2025

https://github.com/open2c/.github

Last synced: 27 Jan 2026