Hi C Python Packages

cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

libbiosmoother

On-the-fly processing and visualization of interactome data.

clodius

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

hicstuff

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

hic2cool

Lightweight converter between hic and cool contact matrices.

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

pypairix

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

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

tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

hiclift

Convert genomic coordinates of contact pairs from one assembly to another.

metator

Metagenomic binning based on Hi-C data

neoloop

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

instagraal

Large genome reassembly based on Hi-C data, continuation of GRAAL

runhic

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

trackc

trackc aims to produce beautiful genome tracks that are highly customizable

pareidolia

Multi-sample change detection in Hi-C patterns

coolpuppy

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

hicpeaks

A Python implementation for BH-FDR and HiCCUPS

biosmoother

On-the-fly processing and visualization of interactome data

diffdomain-py3

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

chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices