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 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.

hic2cool

Lightweight converter between hic and cool contact matrices.

chromosight

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

pypairix

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

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

mustache-hic

Mustache is a Hi-C analysis tool

hiclift

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

metator

A pipeline for binning metagenomic datasets from metaHiC data.

coolpuppy

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

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

neoloop

Predict neo-loops induced by structural variations

biosmoother

On-the-fly processing and visualization of interactome data

chess-hic

Quantitative comparison and automatic feature extraction for chromatin contact data.

hicpeaks

A Python implementation for BH-FDR and HiCCUPS

diffdomain-py3

DiffDomain can test the significant difference of TADs on chromatin.

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

pareidolia

Multi-sample change detection in Hi-C patterns