Pinned Repositories
rtd-tutorial
R2DT
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
2023_Hatfield_Proxisome
Figures and analysis of DMS/PAIR-MaP data from "RNA as a proxisome"
deltaSHAPE
SHAPE-MaP both measures RNA flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. The deltaSHAPE framework incorporates these uncertainties to allow detection of RNA structural differences between any two states, including the general effect of the cellular environment, protein binding in cells, and pathway-dependent RNA conformational changes.
longleaf-dotfiles
Configuration and installation on the Longleaf computing cluster.
QuShape
QuShape enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
RNAvigate
Very flexible tools for plotting and analyzing all kinds of RNA structure data
shapemapper2
Public repository for ShapeMapper 2 releases
Superfold
SuperFold is a pipeline that uses output data from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.