HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data

Tiantian Ye; Yangyang Hu; Sydney Pun; Wenxiu Ma

doi:10.1093/bioinformatics/btad154

HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data

Bioinformatics. 2023 Apr 3;39(4):btad154. doi: 10.1093/bioinformatics/btad154.

Authors

Tiantian Ye¹, Yangyang Hu², Sydney Pun², Wenxiu Ma¹

Affiliations

¹ Department of Statistics, University of California Riverside, Riverside, CA 92521, United States.
² Department of Computer Science and Engineering, University of California Riverside, Riverside, CA 92521, United States.

Abstract

Summary: HiCube is a lightweight web application for interactive visualization and exploration of diverse types of genomics data at multiscale resolutions. Especially, HiCube displays synchronized views of Hi-C contact maps and 3D genome structures with user-friendly annotation and configuration tools, thereby facilitating the study of 3D genome organization and function.

Availability and implementation: HiCube is implemented in Javascript and can be installed via NPM. The source code is freely available at GitHub (https://github.com/wmalab/HiCube).

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Genome*
Genomics*
Software

Grants and funding

R35 GM133678/GM/NIGMS NIH HHS/United States