Customizable workflows based on snakemake and python for the analysis of NGS data

A cool place to store your Hi-C

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

Accurate and flexible loops calling tool for 3D genomic data.

Extract 3D contacts (.pairs) from sequencing alignments

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…

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

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

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

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

Lightweight converter between hic and cool contact matrices.

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

A novel genome assembly pipeline based on deep learning

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

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

Chromosome polymer simulations and in silico capture experiments

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

A Python implementation for BH-FDR and HiCCUPS

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

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