Hypergraph Analysis Toolbox (HAT)

HAT is a software library available for hypergraph analytics. It is available in Python and MATLAB, and we are actively working to maintain and grow the software. The main page and documentation for HAT and a short manuscript detailing its initial features are available at the following links:

Main Page:


To contribute, report a bug, or for additional information on HAT please contact Joshua Pickard at



The 4DNvestigator is a MATLAB toolbox that analyzes time-series genome-wide chromosome conformation capture (Hi-C) and gene expression (RNA-seq) data. The toolbox is available at:

Last updated: 10/24/2019


Install 4DNvestigator by downloading the GitHub files (see link above) and opening fdn.mlapp within MATLAB. Example scripts are also provided through GitHub, and can be run outside of the full MATLAB application.

Help / Report Bugs

For additional support or to report bugs, email Scott Ronquist at

4D Nucleome Analysis Toolbox


The 4D Nucleome Analysis Toolbox (4D NAT) includes functions to load Hi-C matrices, Hi-C read data, and RNA-seq from text files, normalize Hi-C data, detect TADs, plot matrices, and explore translocations. Example scripts are available at:

Last updated: 5/13/2017


Install 4D NAT by downloading the GitHub files (see link above) and double clicking 4DNucleomeAanalysisToolbox.mltbx. Run examples by downloading .m files, opening them and running in MATLAB. Suggested order: Load_Normalize.m, Tad_methods.m, TranslocationAnalysis_100kb.m, TranslocationAnalysis_read.m, PhasePlane.m

Help / Report Bugs

Check to make sure the toolbox is installed by looking at: Home/Add-Ons/Manage Add-Ons and verifying that the tool box is listed there. If it is not, double click on the toolbox to install. For additional support or to report bugs, email Laura Seaman at

Spectral Identification of Topological Domains


We provide a computationally efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level.

Last updated: 5/5/2016


Install the spectral identification algorithm by downloading the ZIP folder here: Spectral Identification of Topological Domains. To verify installation, run the example script Test_Algorithm.m

Help / Report Bugs

For additional support or to report bugs, email Jie Chen at