Abstract
Multiway chromatin interactions are essential for precise transcriptional regulation. Split-Pool Recognition of Interactions by Tag Extension (SPRITE) captures these interactions, which are typically visualized as pairwise heatmaps, where each bin represents one or more multiway contacts. Accurate representation requires downweighting and additional processing to avoid overrepresentation of pairwise signals. However, existing tools such as Juicebox lack the ability to adjust these parameters, leading to biased visualizations. To address this limitation, we introduce MultiVis, a user-friendly, interactive tool for precise and unbiased three-dimensional (3D) genome visualization. MultiVis also generates gene names without requiring external annotation files and allows users to select regions of interest to retrieve corresponding cluster information, thereby removing technical barriers for wet-lab biologists. By enabling real-time analysis, MultiVis accelerates genomics research and advances the study of 3D genome architecture and gene regulation.