geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.

Motivation: The three-dimensional organization of the genome plays a critical role in regulating gene expression by shaping the spatial and temporal interactions between regulatory elements. High-throughput chromosome conformation capture (Hi-C) technologies, along with immunoprecipitation- or chromatin accessibility-based chromatin architecture mapping methods, enable the measurement of chromatin dynamics at both bulk and single-cell levels. However, effectively exploring and comparing chromatin structures remains challenging, particularly when integrating multiple layers of genomic annotation or comparing structural dynamics across conditions. While several tools support interactive 3D genome visualization, few provide a flexible, R-integrated framework that supports custom annotations, side-by-side comparison of multiple stages or conditions, and deployment in Shiny applications. Results: To address this need, we have developed geomeTriD, an R/Bioconductor package that enables interactive visualization of chromatin structures using three.js, supports multi-layer annotation, allows parallel comparison of two chromatin states, and is compatible with Shiny-based analysis workflows. As multi-omic and spatial genomic datasets grow in complexity, GeomeTriD will facilitate the reconstruction and comparison of 3D genome structures across conditions, linking chromatin architecture to gene regulation, epigenetic states, and cell-state transitions. Availability and implementation: geomeTriD is freely available at https://bioconductor.org/packages/geomeTriD.