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RBrowser User Interface

RBrowser UI

1. Overview

The RNA Browser UI is divided into five key regions:

  1. Toolbar (top) – Global menus and controls
  2. Sidebar Views (left) – Track management and annotations
  3. Main Browser View (center) – Continuous, RNA-centric signal display
  4. Plugin System (right) – Extensible panels for structures and interactions
  5. Status Bar (bottom) – Coordinates, load status, and notifications

2. Toolbar

  • Menus: File, Data, Tracks, Selection, Edit, View, Help

3. Sidebar Views

  • Search: Provides a global search box to locate genes, transcripts, coordinates, or keywords across loaded datasets.
  • Track: Manages all data tracks that render within the main browser.
  • Region: Enables precise control over the genomic range displayed.
  • Bookmark: Save and organize regions of interest for later review.
  • History: Keeps a chronological log of your actions within the session.
  • DataHub: Interface to external data sources and repositories.
  • Plugin: List and configure optional extensions that enhance the core browser.

4. Main Browser View

  • Annotation Channel
    RNA annotations channel: single-molecule mods, m6A, Ψ, exon, junction, CCRE, RBP, eQTL, sQTL and Other singals
  • Expand Channel
    Expand each channel to view per-sample datasets (e.g. HeLa, HEK293T, HSC d0/d3/d6/d9)
  • Controls
    Collapse/expand, remove, adjust opacity or color mapping
  • RNA-Centric Signals
    Converts discrete DNA-coordinate features into smooth, continuous tracks focused on transcript coordinates
  • Isoform Visualization
    Exons and junctions rendered as arrowed segments indicating structure & direction
  • Multi-track Overlay
    Vertically stacked tracks for side-by-side comparison of binding, structure, modifications, splicing
  • Interactive Navigation
    Click-and-drag panning, scroll-wheel zooming, real-time redraws

5. Plugin System

  • RNA 2D Structure
  • Secondary-structure diagram; zoom, pan & export
  • RNA 3D Structure
  • Interactive 3D folding model with rotation controls
  • Chromatin-Associated RNA
  • 3D view of RNA–chromatin contacts
  • RNA Interaction Network
  • Graph of RNA–RNA and RNA–protein interactions; nodes color-coded by molecule type (protein, miRNA, lncRNA, mRNA, ncRNA)

6. Status Bar

  • Coordinates & Scale
  • Displays chromosome, start–end positions, and zoom scale (bp/pixel)
  • Load & Cache Status
  • Icons/text for data-loading progress, cache hits, thread utilization

RNA Browser transforms discrete genomic coordinates into a unified, RNA-focused visualization framework. By integrating multi-modal annotations and extensible plugins—spanning secondary and tertiary RNA structures through interaction networks—it provides researchers with an intuitive, high-resolution platform for exploring RNA–DNA crosstalk and transcriptome regulation.