Skip to content

@Weeks-UNC Weeks Lab

Change the repository type filter

All

    Repositories list

    21 repositories

    • RNAvigate

      Public
      Very flexible tools for plotting and analyzing all kinds of RNA structure data
      Python
      •
      MIT License
      •0•10•7•0•Updated Dec 10, 2024Dec 10, 2024

    • shapemapper2

      Public
      Public repository for ShapeMapper 2 releases
      C++
      •
      Other
      •16•32•23•0•Updated Dec 4, 2024Dec 4, 2024

    • RingMapper

      Public
      Code for performing RING-MaP and PAIR-MaP analysis
      Python
      •
      MIT License
      •4•2•2•0•Updated Nov 23, 2024Nov 23, 2024

    • small-scripts

      Public
      Small scripts for common tasks.
      HTML
      •4•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • Superfold

      Public
      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.
      Python
      •
      Other
      •6•2•4•1•Updated Oct 7, 2024Oct 7, 2024

    • fpocketR

      Public
      Program to find drug-like RNA-ligand binding pockets.
      Python
      •
      MIT License
      •0•0•2•0•Updated Sep 17, 2024Sep 17, 2024

    • shapemapper-txome

      Public
      Wrapper for running ShapeMapper2 on large numbers of transcript targets.
      Python
      •0•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • longleaf-dotfiles

      Public
      Configuration and installation on the Longleaf computing cluster.
      Python
      •0•2•0•0•Updated Feb 7, 2024Feb 7, 2024

    • RNAvigate_figures

      Public
      Data and Jupyter notebooks used in the creation of figures for RNAvigate publication.
      publicationsfigures
      HTML
      •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • 2023_Veenbaas_PNAS_fpocketR_Frag-MaP

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 26, 2023Oct 26, 2023

    • 2023_Hatfield_Proxisome

      Public
      Figures and analysis of DMS/PAIR-MaP data from "RNA as a proxisome"
      HTML
      •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

    • RNATools

      Public
      Python
      •2•1•0•0•Updated Jun 15, 2023Jun 15, 2023

    • deltaSHAPE

      Public
      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 …
      Python
      •6•4•0•1•Updated Apr 7, 2023Apr 7, 2023

    • arcPlot

      Public
      Code for plotting arcs
      Python
      •
      MIT License
      •3•1•0•0•Updated Aug 24, 2022Aug 24, 2022

    • ShapeJumper_V1

      Public
      Identifies and processes deletions from illumina sequencing reads
      Python
      •0•0•0•0•Updated May 19, 2021May 19, 2021

    • StructureAnalysis

      Public
      Collection of Scripts to Analyze 2º and 3º RNA Structure
      Python
      •1•2•0•0•Updated May 17, 2021May 17, 2021

    • QuShape

      Public
      QuShape enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
      Python
      •
      Other
      •1•1•2•0•Updated Jun 22, 2020Jun 22, 2020

    • differential-SHAPE

      Public
      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.
      Python
      •0•0•0•0•Updated Jun 22, 2020Jun 22, 2020

    • ShapeMapper_v1.2

      Public
      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.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 16, 2020Jun 16, 2020

    • tombo

      Public
      Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
      Python
      •
      Other
      •54•0•0•0•Updated Feb 22, 2019Feb 22, 2019

    • igv

      Public
      Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
      Java
      •
      MIT License
      •387•0•0•0•Updated Apr 19, 2018Apr 19, 2018