SIMBA3D is a statistical method to infer the 3D chromosome structure from single-cell Hi-C data [preprint]

GINOM is a statistical framework for assessing interval overlap of multiple genomic features [manuscript]

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data [manuscript] [RepEnrich 2.0 is now available!]

CORaL is a software application for comparing expression profiles across experiments by using the rank of genes in the different datasets [manuscript]

GenArch is a method for whole genome 3D reconstruction from single-cell Hi-C data

3DC-Browser is a visualization and annotation tool for 3D structures of chromosomes

FISH-MDS Multidimensional scaling (MDS) for chromosome structure inference from chromosome conformation capture (3C) techniques, with constraints from Fluorescence In Situ Hybridization (FISH)