HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

SALSA: A tool to scaffold long read assemblies with Hi-C data

A GAN-based method for Enhancing Hi-C data

Extract Sequence from Genome According to Annotation File

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

Blazing fast toolkit to work with .hic and .cool files

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

High-performance stochastic modeling of DNA loop extrusion interactions

Phasing and scaffolding polyploid genomes based on Pore-C or Hi-C.

3DGB is a workflow to build 3D models of genomes from HiC data

Tools for processing HIC data.

Python bindings for hictk: read and write .cool and .hic files directly from Python

I'm sharing my automation of the 3D_DNA and SALSA Hi-C scaffolding pipelines.

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

A Nextflow DSL2 pipeline for pretext generation in curation