HAT: Hypergraph analysis toolbox

Joshua Pickard; Can Chen; Rahmy Salman; Cooper Stansbury; Sion Kim; Amit Surana; Anthony Bloch; Indika Rajapakse

doi:10.1371/journal.pcbi.1011190

HAT: Hypergraph analysis toolbox

PLoS Comput Biol. 2023 Jun 5;19(6):e1011190. doi: 10.1371/journal.pcbi.1011190. eCollection 2023 Jun.

Authors

Joshua Pickard^{1

2}, Can Chen³, Rahmy Salman⁴, Cooper Stansbury¹, Sion Kim⁴, Amit Surana⁵, Anthony Bloch⁶, Indika Rajapakse^{1

2

6}

Affiliations

¹ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
² iReprogram, Inc., Ann Arbor, Michigan, United States of America.
³ Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
⁴ Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America.
⁵ Raytheon Technologies Research Center, East Hartford, Connecticut, United States of America.
⁶ Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America.

Abstract

Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized to precisely represent and analyze multi-way interactions. Here we present the Hypergraph Analysis Toolbox (HAT), a software package for visualization and analysis of multi-way interactions in complex systems.

Copyright: © 2023 Pickard et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

MeSH terms

Chromosomes*
Software*

Grants and funding

This work is supported in part by the Air Force Office of Scientific Research (AFOSR) awards FA9550-18-1-0028 and FA9550-22-1-0215 (IR), NSF DMS2103026 (AB), and a MathWorks Fellowship to the Rajapakse Lab (IR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.