geomeTriD

geomeTriD enables interactive visualization of three-dimensional chromatin structures and supports integration of multi-layer genomic annotations, parallel comparison of chromatin states, and deployment in Shiny-based analysis workflows.

Key Features:

• Interactive 3D Visualization: Renders chromatin structures using WebGL-based three.js or the rgl rendering library.
• Multi-layer Annotation Support: Integrates multiple layers of genomic annotation with 3D structural models.
• Parallel Comparison: Allows side-by-side comparison of two chromatin states or conditions.
• Shiny Compatibility: Generates dynamic 3D plots and HTML widgets compatible with Shiny applications.

Scientific Applications:

• Chromatin Structure Exploration: Identifies and explores spatial chromatin patterns within genomic regions.
• Structural Dynamics Comparison: Compares chromatin structural dynamics across different conditions and data types.
• Gene Regulation Analysis: Links chromatin architecture to gene regulation, epigenetic states, and cell-state transitions.
• Hi-C Data Integration: Visualizes chromatin organization from high-throughput chromosome conformation capture technologies.
• Single-cell Chromatin Analysis: Supports visualization of chromatin dynamics measured at single-cell levels.

Methodology:

geomeTriD is implemented as an R/Bioconductor package that uses three.js for interactive 3D rendering.