R2DT
latest
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 and Python package
API
Python package
Running r2dt-client in Google Colab
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
Index
Edit on GitHub
Index
Read the Docs
v: latest
Versions
latest
develop
Downloads
On Read the Docs
Project Home
Builds