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    • Wrapper for running and plotting trees using CellPhy
      R
      MIT License
      0000Updated Apr 13, 2026Apr 13, 2026
    • ASAP

      Public
      WGS Analysis Pipeline
      Nextflow
      MIT License
      0100Updated Apr 3, 2026Apr 3, 2026
    • PTATO

      Public
      PTa Analysis TOolkit
      R
      MIT License
      51580Updated Mar 2, 2026Mar 2, 2026
    • A distributed framework for running Cellphy
      Nextflow
      2000Updated Feb 17, 2026Feb 17, 2026
    • R package for extracting and visualizing mutational patterns in base substitution catalogues
      R
      MIT License
      45920Updated Feb 16, 2026Feb 16, 2026
    • SMuRF

      Public
      Somatic Mutations Rechecker and Filtering
      Python
      MIT License
      3411Updated Dec 5, 2024Dec 5, 2024
    • NF-IAP

      Public
      Illumina Analysis Pipeline in Nextflow
      Nextflow
      MIT License
      5200Updated Oct 8, 2024Oct 8, 2024
    • NF-SMuRF

      Public
      Somatic Mutations Rechecker and Filtering
      Nextflow
      MIT License
      0000Updated Mar 15, 2024Mar 15, 2024
    • Tool to design primers on a vcf file (using primer3 software)
      C
      MIT License
      4711Updated May 22, 2023May 22, 2023
    • Walker

      Public
      Link germline mutations with somatic variants
      Python
      MIT License
      0000Updated Apr 7, 2023Apr 7, 2023
    • Python
      0001Updated Dec 26, 2022Dec 26, 2022
    • Utility scripts for elabjournal
      Python
      1100Updated Aug 10, 2022Aug 10, 2022
    • Data and code accompanying the research protocol: "Assessing the mutagenic impact of genotoxins in human umbilical cord-blood derived stem cells"
      R
      1000Updated Apr 8, 2022Apr 8, 2022
    • R
      0000Updated Feb 23, 2022Feb 23, 2022
    • Scripts to analyze targeted sequencing data
      R
      MIT License
      0000Updated Dec 29, 2021Dec 29, 2021
    • R
      1000Updated Jul 17, 2020Jul 17, 2020
    • Scripts to perform mutational signature refitting
      R
      MIT License
      0000Updated Jun 9, 2020Jun 9, 2020
    • RNASeq-NF

      Public
      RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
      Nextflow
      8000Updated May 26, 2020May 26, 2020
    • R
      5100Updated Apr 24, 2020Apr 24, 2020
    • IAP

      Public
      Illumina analysis pipeline
      Perl
      MIT License
      15000Updated Apr 2, 2020Apr 2, 2020
    • Mutational signature selection and refitting pipeline
      R
      2000Updated Sep 6, 2019Sep 6, 2019
    • INDELFI

      Public
      Script for INDEL filtering
      Perl
      1000Updated Apr 25, 2019Apr 25, 2019
    • Identify mutations that are clonally present in a clone but subclonally present in a bulk sample
      R
      1000Updated Mar 28, 2019Mar 28, 2019
    • Combines CallableLoci bed files from control and experimental samples.
      Python
      1000Updated Mar 28, 2019Mar 28, 2019
    • Filter SNVs or Indels based on non genotype specific quality parameters.
      Python
      1000Updated Mar 28, 2019Mar 28, 2019
    • SNVFI

      Public
      Single Nucleotide Variant Filtering
      Shell
      1100Updated Feb 12, 2019Feb 12, 2019
    • smMIPfil

      Public
      script for smMIP data analysis
      Perl
      1000Updated Jun 1, 2018Jun 1, 2018
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