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    14 repositories

    • wf-ml-markers-senescence

      Public
      Detecting cellular senescence using transcriptomic and proteomic data.
      Python
      •0•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • wf-module-dorado

      Public
      A snakemake workflow that is intended to be consumed by other workflows allowing basecalling of Oxford Nanopore files with dorado
      Python
      •
      Other
      •0•0•0•1•Updated Mar 6, 2026Mar 6, 2026

    • rnakinet

      Public
      RNAkinet: Detect 5eu-modified reads directly from the raw nanopore sequencing signal to quantify RNA kinetics
      Python
      •
      Other
      •0•5•0•0•Updated Mar 4, 2026Mar 4, 2026

    • tabletools

      Public
      Miscellaneous scripts for manipulating table files
      Python
      •
      Other
      •5•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • nanoplen

      Public
      Package for the analysis of the nanopore read lengths, e.g. to calculate the significant differential transcript length.
      R
      •
      Other
      •2•3•0•1•Updated Sep 26, 2025Sep 26, 2025

    • wf-module-ensembl

      Public
      A snakemake workflow that is intended to be consumed by other workflows allowing download of ENSEMBL reference files
      Python
      •
      Other
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • rnakinet-pub

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Mar 28, 2025Mar 28, 2025

    • lab-tools

      Public
      Scripts for processing low-throughput molecular biology data
      R
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • samql

      Public
      SQL-like query language for the SAM/BAM file format
      gobioinformaticssql
      gobioinformaticssqlsequencingsambam
      Go
      •
      MIT License
      •5•29•0•0•Updated Sep 20, 2023Sep 20, 2023

    • Hackathon202305

      Public
      Our first hackathon! Training for mRNA decay rates
      Jupyter Notebook
      •1•0•0•0•Updated May 24, 2023May 24, 2023

    • senescence-omics

      Public
      Source code for manuscript "Senescence-specific translation dysregulation desensitizes cells to stress by inhibiting activation of the integrated stress respons…
      R
      •0•0•0•0•Updated Apr 20, 2023Apr 20, 2023

    • mouse_liver

      Public
      Collaboration with Payel Sen
      Python
      •
      Other
      •1•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • bioutils

      Public
      Standalone utility scripts for bioinformatics
      Perl
      •4•1•0•0•Updated Feb 28, 2022Feb 28, 2022

    • samutils

      Public
      Standalone utility scripts for manipulating SAM files
      Perl
      •2•0•0•0•Updated Dec 10, 2020Dec 10, 2020