R2DT
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About R2DT

  • R2DT documentation
  • Method overview
    • Pipeline

Getting started

  • Installation
    • Setup a development environment
    • Manual installation
  • Command line reference
    • Output files
    • Manually selecting template type
    • Manually selecting specific template
    • Constraint-based folding for insertions
    • Template-free visualisation
    • Skipping ribovore filters
    • Other useful commands
  • Annotations and data layers
    • Alignment accuracy
    • Example annotation file
    • Example color scheme file
    • Example R2DT commands
    • Displaying other types of data
  • Editing R2DT diagrams
    • RNAcanvas
    • XRNA-React
      • Constraint modes
      • Formatting 2D layouts
    • SVG editors
    • RNA 2D JSON Schema
  • API
  • Embeddable widget
    • Live example

Updating R2DT

  • Creating and updating templates
    • Adding new templates
    • Manually creating templates
      • Creating templates using FASTA/BPSEQ and Traveler XML files
      • Creating templates using RNA 2D JSON Schema files
      • Other ways of creating templates
    • Updating Rfam templates
  • Updating documentation
  • Testing
    • Useful commands
    • Updating example files
  • Base and R2DT Docker Images
    • Overview
    • Base Image
    • R2DT Image
    • Upgrade Process
  • Release process
    • git workflow
      • Normal development
        • Small features: single commits can be made to develop
        • Big features: keeping up to date with develop
      • Making a release
      • Fixing bugs: “hotfix” branches
      • Summary of main principles
        • Much of the text above was borrowed and modified with permission from Sean Eddy, from the HMMER GitHub repository.

Project info

  • Team
    • Contributors
    • Acknowledgements
  • News and releases
    • R2DT Version 1.4
      • Visualising alignment accuracy
      • Displaying pseudoknots
      • Template-free display
      • New templates
      • Other updates
      • Teamwork makes the dream work
      • Summary
    • Displaying detailed RNA secondary structure at PDBe entry pages
    • R2DT Version 1.3
      • Constrained folding
      • Other updates
      • Summary
    • RNA topology viewer added to PDBe pages
    • R2DT paper is out in Nature Communications
    • R2DT is officially launched
    • Biorxiv preprint
    • LSU structures using single-page layouts
    • Rfam families visualised with R2DT
    • First R2DT structures are live
R2DT
  • News and releases
  • Edit on GitHub

News and releases

  • R2DT Version 1.4
  • Displaying detailed RNA secondary structure at PDBe entry pages
  • R2DT Version 1.3
  • RNA topology viewer added to PDBe pages
  • R2DT paper is out in Nature Communications
  • R2DT is officially launched
  • Biorxiv preprint
  • LSU structures using single-page layouts
  • Rfam families visualised with R2DT
  • First R2DT structures are live
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