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    43 repositories

    • rr_util

      Public
      Utilities for generating raw reads datasets for deep neural network training
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • m2_util

      Public
      Utilities to extra mutate-and-map 2D maps from big library sequencing runs
      Python
      •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • ubr

      Public
      Ultraplex-Bowtie2-RNAframework pipeline for analysis of SHAPE-MaP/DMS-MaP big library runs
      MATLAB
      •
      MIT License
      •0•3•0•0•Updated Feb 10, 2025Feb 10, 2025

    • daslab_tools

      Public
      Tools, mainly for cluster usage, for Das lab at Stanford
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 8, 2025Feb 8, 2025

    • arnie

      Public
      Python utility to estimate, compare, and reweight RNA energetics across many secondary structure algorithms.
      Python
      •
      MIT License
      •31•101•8•0•Updated Feb 1, 2025Feb 1, 2025

    • Server_Primerize

      Public
      Primerize PCR Assembly Design Server
      HTML
      •
      Other
      •1•2•0•0•Updated Jan 31, 2025Jan 31, 2025

    • KaggleOpenVaccine

      Public archive
      Jupyter Notebook
      •
      MIT License
      •7•54•0•0•Updated Sep 11, 2024Sep 11, 2024

    • draw_rna

      Public
      Draw RNA secondary structures in python.
      Jupyter Notebook
      •
      MIT License
      •15•46•6•3•Updated Sep 3, 2024Sep 3, 2024

    • CASP15_RNA_EM

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•2•0•Updated Aug 16, 2024Aug 16, 2024

    • Server_RMDB

      Public
      RNA Mapping Database
      JavaScript
      •
      Other
      •5•4•44•0•Updated Aug 5, 2024Aug 5, 2024

    • KaggleRibonanza

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 15, 2024Jun 15, 2024

    • Coronavirus_SL5_3D

      Public
      Accompanying the publication: Tertiary folds of the SL5 RNA from the 5’ proximal region of SARS-CoV-2 and related coronaviruses
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 13, 2024May 13, 2024

    • big_library_design

      Public
      Python
      •
      MIT License
      •0•0•24•0•Updated Mar 5, 2024Mar 5, 2024

    • DataPrepRibonanzaKaggle2023

      Public archive
      Scripts and example files -- data preparation for Kaggle Ribonanza competition 2023. To be publicly released after competition end.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Feb 25, 2024Feb 25, 2024

    • casp-rna

      Public archive
      Pipeline used to assess RNA in CASP15
      Jupyter Notebook
      •2•3•0•0•Updated Nov 15, 2023Nov 15, 2023

    • RMDB_DataWrangle

      Public archive
      Wrangle RDATs from RMDB into single .csv for machine learning training
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • Stanford_BIOC202_DataScience

      Public archive
      Support repository for Stanford BIOC202 data science bootcamp session
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • RiboGraphViz

      Public
      Visualize global properties of large RNAs using GraphViz force-directed layout.
      Jupyter Notebook
      •
      MIT License
      •8•20•2•1•Updated Sep 7, 2023Sep 7, 2023

    • Server_Daslab

      Public
      Das Lab Website
      HTML
      •
      Other
      •3•1•5•3•Updated Mar 8, 2023Mar 8, 2023

    • smiFISH-Probes

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 12, 2022Sep 12, 2022

    • rna_benchmark

      Public archive
      Python scripts & reference data for Rosetta RNA modeling benchmarks
      Scala
      •1•7•4•0•Updated Sep 8, 2022Sep 8, 2022

    • FARFAR2_modeling_examples

      Public archive
      Modeling examples for FARFAR2
      Scala
      •
      MIT License
      •0•3•0•0•Updated Aug 19, 2022Aug 19, 2022

    • openvaccine-CE-analysis

      Public archive
      Data and analysis of capillary electrophoresis data measuring mRNA degradation rates for Combinatorial Optimization of mRNA paper, Das and Barna labs (2020).
      Jupyter Notebook
      •
      MIT License
      •2•10•0•0•Updated Nov 15, 2021Nov 15, 2021

    • RNA-deg-rates

      Public archive
      Degradation rates for RNA molecules compiled during Stanford OpenVaccine research, 2020-2021
      MATLAB
      •1•1•0•0•Updated Nov 8, 2021Nov 8, 2021

    • 3-UTR-Quantification

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Aug 14, 2021Aug 14, 2021

    • zetafold

      Public archive
      Sandbox for secondary structure modeling
      Python
      •
      MIT License
      •1•3•9•0•Updated Aug 3, 2021Aug 3, 2021

    • CDSfold_SU

      Public
      Update CDSfold to modern C++ while maintaining performance
      C++
      •
      Other
      •0•3•10•0•Updated Jul 15, 2021Jul 15, 2021

    • SARS_CoV-2_shape_comparison

      Public archive
      SARS-CoV-2 whole-genome chemical reactivity heatmap
      Jupyter Notebook
      •2•0•0•0•Updated Jun 23, 2021Jun 23, 2021

    • ToyFold-1D

      Public archive
      Testing calculations for simple Toyfold RNA folding model in 1D
      Rich Text Format
      •
      MIT License
      •1•0•0•0•Updated Mar 22, 2021Mar 22, 2021

    • FARFAR2-Apo-Riboswitch

      Public archive
      Models of apo riboswitches generated by FARFAR2
      Other
      •0•3•0•0•Updated Feb 8, 2021Feb 8, 2021