Pinned Repositories
arcPlot
Code for plotting arcs
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.
fpocketR
Program to find drug-like RNA-ligand binding pockets.
longleaf-dotfiles
Configuration and installation on the Longleaf computing cluster.
RingMapper
Code for performing RING-MaP and PAIR-MaP analysis
RNATools
RNAvigate
Very flexible tools for plotting and analyzing all kinds of RNA structure data
shapemapper2
Public repository for ShapeMapper 2 releases
StructureAnalysis
Collection of Scripts to Analyze 2º and 3º RNA Structure
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.
Weeks Lab's Repositories
Weeks-UNC/shapemapper2
Public repository for ShapeMapper 2 releases
Weeks-UNC/RNAvigate
Very flexible tools for plotting and analyzing all kinds of RNA structure data
Weeks-UNC/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.
Weeks-UNC/longleaf-dotfiles
Configuration and installation on the Longleaf computing cluster.
Weeks-UNC/StructureAnalysis
Collection of Scripts to Analyze 2º and 3º RNA Structure
Weeks-UNC/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.
Weeks-UNC/arcPlot
Code for plotting arcs
Weeks-UNC/QuShape
QuShape enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
Weeks-UNC/RingMapper
Code for performing RING-MaP and PAIR-MaP analysis
Weeks-UNC/RNATools
Weeks-UNC/2023_Hatfield_Proxisome
Figures and analysis of DMS/PAIR-MaP data from "RNA as a proxisome"
Weeks-UNC/2023_Veenbaas_PNAS_fpocketR_Frag-MaP
Weeks-UNC/differential-SHAPE
The differential SHAPE experiment uses three reagents, the workhorse 1M7, plus NMIA and 1M6 which together detect higher-order and noncanonical interactions. Among other uses, the resulting three-reagent SHAPE experiment makes possible very accurate modeling of RNA secondary structure.
Weeks-UNC/fpocketR
Program to find drug-like RNA-ligand binding pockets.
Weeks-UNC/RNAvigate_figures
Data and Jupyter notebooks used in the creation of figures for RNAvigate publication.
Weeks-UNC/ShapeJumper_V1
Identifies and processes deletions from illumina sequencing reads
Weeks-UNC/shapemapper-txome
Wrapper for running ShapeMapper2 on large numbers of transcript targets.
Weeks-UNC/small-scripts
Small scripts for common tasks.
Weeks-UNC/igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
Weeks-UNC/ShapeMapper_v1.2
This software has been completely rewritten. Please, use shapemapper2, unless you have a good reason to use this instead. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
Weeks-UNC/tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.