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

Extract Sequence from Genome According to Annotation File

A GAN-based method for Enhancing Hi-C data

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

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

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

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

High-performance stochastic modeling of DNA loop extrusion interactions

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

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

Tools for processing HIC data.

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

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

A Nextflow DSL2 pipeline for pretext generation in curation

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