Hi C Python Packages

cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

hicstuff

Simple library/pipeline to generate and handle Hi-C data.

libbiosmoother

On-the-fly processing of interactome data

hic2cool

Lightweight converter between hic and cool contact matrices.

clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

trackc

trackc aims to produce beautiful genome tracks that are highly customizable

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

runhic

An easy-to-use Hi-C data processing software supporting distributed computation.

chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

mustache-hic

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

hiclift

A fast and efficient tool for converting chromatin interaction data between genome assemblies

metator

Metagenomic binning based on Hi-C data

coolpuppy

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

pypairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

neoloop

Predict neo-loops induced by structural variations

hicpeaks

A Python implementation for BH-FDR and HiCCUPS

diffdomain-py3

DiffDomain is a statistically sound method for detecting differential TADs between conditions

pareidolia

Multi-sample change detection in Hi-C patterns

chess-hic

Quantitative comparison and automatic feature extraction for chromatin contact data.

biosmoother

On-the-fly processing and visualization of interactome data

instagraal

Large genome reassembly based on Hi-C data

stripepy-hic

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning