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    39 repositories

    • crosslinking

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • VIECPLX

      Public
      C++
      •0•1•0•0•Updated Mar 6, 2025Mar 6, 2025

    • negseeddesign

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • ViennaRNA

      Public
      The ViennaRNA Package
      C
      •
      Other
      •81•343•40•4•Updated Oct 20, 2024Oct 20, 2024

    • RNAcode

      Public
      RNAcode - Detecting protein coding genes in multiple sequence alignment
      C
      •
      GNU General Public License v3.0
      •8•25•6•1•Updated Aug 22, 2024Aug 22, 2024

    • RNAblueprint

      Public
      RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints
      designrna-structurerna-designriboswitchinverse-foldingviennarnanupackrnablueprint-library
      C++
      •
      GNU General Public License v3.0
      •3•10•1•0•Updated Jul 29, 2024Jul 29, 2024

    • fornac

      Public
      A container for the forna visualization software.
      JavaScript
      •
      Apache License 2.0
      •14•18•14•1•Updated May 30, 2024May 30, 2024

    • RRIdesign

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 27, 2024Mar 27, 2024

    • forgi

      Public
      An RNA manipulation library.
      Python
      •
      GNU General Public License v3.0
      •31•56•13•0•Updated Feb 16, 2024Feb 16, 2024

    • ernwin

      Public
      Sample and predict coarse grain 3D RNA structures
      Python
      •
      GNU Affero General Public License v3.0
      •5•9•3•0•Updated Feb 12, 2024Feb 12, 2024

    • drtransformer

      Public
      Heuristic cotranscriptional folding using the nearest neighbor energy model.
      Python
      •
      MIT License
      •5•5•1•0•Updated Sep 11, 2023Sep 11, 2023

    • drforna

      Public
      Interactive visualization of cotranscriptional folding
      rnasecondary-structurecotranscriptional-foldingvisualization
      JavaScript
      •
      Apache License 2.0
      •2•7•4•0•Updated Aug 3, 2023Aug 3, 2023

    • softconsensus

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 23, 2023Jun 23, 2023

    • salty

      Public
      Tutorial like notebook to use salt option in RNAlib
      Jupyter Notebook
      •0•1•0•0•Updated Jun 8, 2023Jun 8, 2023

    • PLfoldSampling

      Public
      RNAPLfold revisited
      Jupyter Notebook
      •0•2•0•0•Updated Jun 6, 2023Jun 6, 2023

    • DrTutorial

      Public
      Data, scripts and other resources for the DrTransformer Tutorial
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•1•0•0•Updated May 16, 2023May 16, 2023

    • ERNWIN-SPQR-Tutorial

      Public
      ERNWIN-SPQR Tutorial files
      Shell
      •0•0•0•0•Updated May 15, 2023May 15, 2023

    • YFVnext

      Public
      Nextstrain community build 'Genomic diversity of Yellow Fever virus (YFV)'
      0•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • VEEnext

      Public
      Nextstrain community build 'Molecular epidemiology of Venezuelan equine encephalitis complex viruses'
      bioinformaticsvirusphylogeneticsphylogeographyepidemiologyvirologyphylodynamicsvenezuelan-equine-encephalitis-virus
      1•1•0•0•Updated Jan 11, 2023Jan 11, 2023

    • CHIKV

      Public
      Nextstrain community build 'Molecular epidemiology of Chikungunya virus'
      phylogeographyepidemiologyvirologyphylodynamicschikungunyabioinformatics
      1•2•0•0•Updated Jan 10, 2023Jan 10, 2023

    • TBEVnext

      Public
      nextstrain.org build: Molecular epidemiology of Tick-borne encephalitis virus (TBEV)
      0•0•0•0•Updated Dec 9, 2022Dec 9, 2022

    • BarMap

      Public
      A pipeline for simulation of RNA folding on dynamic landscapes
      Perl
      •3•0•0•2•Updated Dec 9, 2022Dec 9, 2022

    • rnadeep

      Public
      Code and data for the RNAML paper
      Python
      •1•8•0•0•Updated Aug 4, 2022Aug 4, 2022

    • pourRNA

      Public
      C++
      •
      GNU General Public License v2.0
      •0•4•1•0•Updated Jul 10, 2022Jul 10, 2022

    • Barriers

      Public
      Compute local minima and energy barriers of a landscape
      C
      •
      GNU General Public License v2.0
      •2•4•0•0•Updated Feb 25, 2022Feb 25, 2022

    • RNAxplorer

      Public
      RNAxplorer - Explore the RNA conformation space through sampling and other techniques
      C
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Dec 17, 2020Dec 17, 2020

    • forna

      Public
      Create force-directed graphs of RNA secondary structures.
      JavaScript
      •
      Apache License 2.0
      •32•102•18•1•Updated Jun 6, 2020Jun 6, 2020

    • rnautils

      Public
      A collection of functionality for manipulating RNA secondary structures.
      JavaScript
      •
      Apache License 2.0
      •0•1•0•1•Updated Apr 29, 2020Apr 29, 2020

    • RNAz

      Public
      RNAz - predicting structural noncoding RNAs
      C++
      •
      Other
      •5•14•4•0•Updated Oct 21, 2019Oct 21, 2019

    • SISSIz

      Public
      SISSIz: Dinucleotide controlled random alignments and RNA gene prediction
      C
      •
      Other
      •3•8•0•0•Updated Jul 25, 2019Jul 25, 2019