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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
    • Processing Stockholm alignments
      • Coloring panels
      • Layout engines
    • Skipping ribovore filters
    • Stitching multiple diagrams
      • Basic usage
      • Sorting by genomic coordinates
      • Adding captions
      • Available options
      • Join glyphs
      • Example with all options
    • 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
    • Exornata
      • Constraint modes
      • Formatting 2D layouts
    • SVG editors
    • RNA 2D JSON Schema
  • API and Python package
    • API
    • Python package
      • Running r2dt-client in Google Colab
  • Embeddable widget
    • Live example

3D structures

  • Visualising RNA from PDB structures
    • Basic usage
    • Using local structure files
    • Choosing a base pair extractor
    • Specifying structure format
    • Extracting a specific chain
    • Output files
    • Examples
    • Missing nucleotides in PDB structures
    • Animating RNA secondary structures
      • Animating from PDB files

Alignments

  • Processing Stockholm alignments
    • Overview
    • Quick start
    • Input format
      • structureID + regionID
      • Format rules
      • Simple alignment (e.g. Rfam seed)
      • WUSS notation
    • Example: HCV structural elements
      • Step 1: Run stockholm command
      • Step 2: View the stitched output
      • Step 3: Use the thumbnail view
        • What the thumbnail removes
    • Command options
    • Output files
    • RF consensus computation
    • Validation and skipping
    • Coloring panels
      • Auto-colour by structure name
      • Auto-colour by genomic region
      • Custom colour palette from a TSV file
      • What gets coloured
  • Annotating viral genomes
    • Overview
    • Quick start
    • Example: SARS-CoV-2 coronavirus
      • Step 1: Prepare input
      • Step 2: Run viral-annotate
      • Step 3: Examine the output
      • Step 4: Create a stitched diagram
    • Two approaches to viral RNA annotation
      • Example: HCV using Stockholm alignment
    • Command reference
      • viral-annotate
      • stitch
    • Understanding the results
      • cmscan.tblout format
      • Genomic coordinates in filenames
    • Advanced usage
      • Using a custom CM library
      • Customising the stitched output
      • Integrating with other R2DT workflows
    • Supported virus families
    • Troubleshooting
      • No hits found
      • cmscan is slow
      • Missing diagrams
    • Gallery
      • SARS-CoV-2 coronavirus
      • Hepatitis C virus (HCV)
      • Dengue virus serotype 2
    • See also
  • Covariation visualisation
    • Motivation
    • Example: GOLLD RNA (PDB 9LEL)
      • R-scape / R2R output (with overlaps)
      • R2DT output (overlap-free, with covariation)
    • Colour scheme
    • How it works
      • Detection
      • Pipeline
    • Usage
      • From an R-scape Stockholm file
      • Running R-scape first
    • Related

Updating R2DT

  • Creating and updating templates
    • Adding new templates
    • Creating templates using RNA 2D JSON Schema files
      • Exornata
      • RNAcanvas
      • Creating templates using FASTA/BPSEQ and Traveler XML files
    • Updating Rfam templates
  • Updating documentation
    • Regenerating doc images
    • Verifying documentation
  • Testing
    • Useful commands
    • Updating example files
  • Docker images
    • Overview
    • Base image
    • Main image
      • Bundled covariance model libraries
    • Upgrade process
    • Building for non-default platforms/architectures
  • GitHub Actions
    • Base image
    • Main image
      • Key steps
      • Parallel builds in Dockerfile
      • Parallel builds in main workflow
    • Tagging workflow
      • Tag base image
  • 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 2.2
      • Highlights
        • New viral-annotate command
        • New stitch command for combined diagrams
        • New pdb command for RCSB structures
        • New stockholm command for multiple sequence alignments
        • RNApuzzler layout engine
        • Insertion arcs for large insertions
        • Covariation visualisation
      • Other improvements
      • Documentation
      • Getting started
      • Links
      • Acknowledgements
    • R2DT Version 2.0 and new preprint
    • 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
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