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

Area of Science:

• Genomics
• Computational Biology
• Bioinformatics

Background:

• The three-dimensional genome organization is crucial for gene expression regulation.
• High-throughput chromosome conformation capture (Hi-C) and other methods map chromatin dynamics.
• Comparing and integrating multi-layer genomic annotations of chromatin structure is challenging.

Purpose of the Study:

• To develop a flexible R-integrated framework for interactive 3D genome visualization and comparison.
• To address limitations in existing tools for exploring chromatin structures across conditions and with custom annotations.

Main Methods:

• Developed geomeTriD, an R/Bioconductor package.
• Utilized three.js for interactive 3D chromatin structure visualization.
• Integrated multi-layer annotation capabilities and side-by-side comparison of chromatin states.
• Ensured compatibility with Shiny-based analysis workflows.

Main Results:

• GeomeTriD provides interactive visualization of chromatin structures.
• The package supports multi-layer genomic annotation.
• It allows parallel comparison of two distinct chromatin states.
• GeomeTriD is compatible with Shiny applications for advanced analysis.

Conclusions:

• GeomeTriD facilitates the reconstruction and comparison of 3D genome structures.
• It links chromatin architecture to gene regulation, epigenetic states, and cell-state transitions.
• The package will aid researchers in analyzing complex multi-omic and spatial genomic datasets.