snhic
Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.
HiCcompare
Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
firecaller
FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data
3d-genome-builder
3DGB is a workflow to build 3D models of genomes from HiC data
genomenote
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.
hictkpy
Python bindings for hictk: read and write .cool and .hic files directly from Python