Open Chromosome Collective

cooler

A cool place to store your Hi-C

bioframe

Genomic interval operations on Pandas DataFrames

cooltools

The tools for your .cool's

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

distiller-nf

A modular Hi-C mapping pipeline

coolpuppy

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

polychrom

Chromosome polymer simulations and in silico capture experiments

quaich

snakemake pipeline for Hi-C post-processing

open2c_examples

cooler-binder

Cooler demo using a Jupyter notebook Binder

looplib

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

inspectro

Hi-C spectral analysis workflow

inspectro-nf

polychrom-hoomd

polykit

open2c_vignettes

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

distiller-sm

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

pairlib

Read, write and analyse Hi-C pairs

assemblyinfo

Genome assembly metadata

MultiQC

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

open2c.github.io

Welcome to the Open Chromosome Collective!

pairtools-1

CLI tools to process mapped Hi-C data

.github

bioframe-poster

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

distiller-test-data

Test data for distiller

gsoc

Google Summer of Code - Open2C

MultiQC_TestData

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

pyfilesplit