multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning

Structured state space sequence models

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

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

GENome Organisation Visual Analytics

Database of computational tools developed by members of the International Nucleome Consortium

Comparison of Hi-C Experiments using Structural Similarity.

FAN-C: Framework for the ANalysis of C-like data

A collection of tools for Hi-C data analysis

The tools for your .cool's

Lightweight converter between hic and cool contact matrices.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder

Chrom3D is a 3D genome modeling platform designed to incorporate a versatile set of constraints. For example, Chrom3D can simultaneously incorporate chromosomal interaction constraints (such as Hi-…

A modular Hi-C mapping pipeline

A cool place to store your Hi-C