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    24 repositories

    • YangLab.github.io

      Public
      CSS
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • Pre-rRNA-spatial-distribution-and-functional-organisation-of-the-nucleolus

      Public
      R
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • eTALED_computational_analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 22, 2025Feb 22, 2025

    • RtABE_computational_analysis

      Public
      Relevant code for analyzing the efficiency and off-target effects of RtABE.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • CIRCexplorer2

      Public
      circular RNA analysis toolset
      circrna
      Python
      •
      Other
      •46•85•19•0•Updated Sep 8, 2024Sep 8, 2024

    • DEMINING

      Public
      DEMINING: a stepwise computational framework to directly detect expressed DNA and RNA mutations in RNA deep sequencing data (DEMINING).
      Shell
      •3•10•6•0•Updated Jul 31, 2024Jul 31, 2024

    • CIRCshapemapper

      Public
      Python
      •2•3•0•0•Updated Jan 19, 2024Jan 19, 2024

    • SCAPTURE

      Public
      Shell
      •
      Other
      •5•19•8•0•Updated Jan 9, 2024Jan 9, 2024

    • Epitranscriptomic-maps-of-5-methylcytosine

      Public
      This is the bioinformatical analysis pipline associated with "Epitranscriptomic maps of 5-methylcytosine reveal substrate diversity of NSUN methyltransferases and links to mRNA translation and turnover"
      Shell
      •0•1•0•0•Updated Dec 29, 2023Dec 29, 2023

    • CFBI

      Public
      CFBI is custom Perl and Shell scripts for base substitution and indel frequencies calculation.
      Perl
      •
      MIT License
      •1•3•0•0•Updated Oct 8, 2023Oct 8, 2023

    • RADAR

      Public
      RADAR is devised to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.
      Perl
      •
      GNU General Public License v3.0
      •8•20•3•0•Updated Oct 8, 2023Oct 8, 2023

    • BEIDOU

      Public
      Base/Prime Editor Induced DNA Off-target site identification Unified toolkit
      Shell
      •2•6•0•0•Updated Oct 8, 2023Oct 8, 2023

    • BEable_circRNA_methods

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2023May 31, 2023

    • RNAlight

      Public
      a machine learning model to identify nucleotide features determining RNA subcellular localization
      Jupyter Notebook
      •
      MIT License
      •2•14•0•0•Updated Mar 11, 2023Mar 11, 2023

    • Nucleolar-URB1-ensures-3-ETS-rRNA-removal-to-prevent-exosome--surveillance

      Public
      ImageJ Macro
      •0•0•0•0•Updated Dec 27, 2022Dec 27, 2022

    • CDCscreen

      Public
      Source code for the computational analysis of functional circular RNAs screening using the CRISPR-Cas13 system
      Shell
      •3•7•0•0•Updated Mar 23, 2022Mar 23, 2022

    • CLEAR

      Public
      direct comparison of circular and linear RNA expression
      Python
      •11•23•11•0•Updated Jan 17, 2021Jan 17, 2021

    • TERate

      Public
      TERate is a computational pipeline to measure transcription elongation rates (TERs) with 4sUDRB-Seq.
      Shell
      •
      MIT License
      •2•5•1•0•Updated Dec 3, 2020Dec 3, 2020

    • bsRNA-seq-m5C

      Public
      Pipeline for m5C calling.
      Perl
      •0•6•0•0•Updated Apr 16, 2020Apr 16, 2020

    • CIRCfinder

      Public
      A pipeline to map junction reads for circular intronic RNAs (ciRNAs)
      circrna
      Python
      •
      MIT License
      •7•5•0•0•Updated Dec 4, 2019Dec 4, 2019

    • CIRCexplorer

      Public
      A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
      circrna
      Python
      •
      Other
      •23•61•2•0•Updated Jun 1, 2019Jun 1, 2019

    • bamTobw

      Public
      Convert BAM files to bigWig files with a simple command
      Shell
      •
      MIT License
      •10•20•0•0•Updated Nov 30, 2018Nov 30, 2018

    • CIRCpseudo

      Public
      Pipeline for circRNA-derived pseudogenes
      Perl
      •
      Other
      •2•2•0•0•Updated Apr 26, 2017Apr 26, 2017

    • CSI

      Public
      Complementary Sequence Index (CSI)
      Python
      •
      Other
      •3•6•1•0•Updated Dec 12, 2016Dec 12, 2016