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@ToolsVanBox Team van Boxtel @ Princess Maxima Center

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    27 repositories

    • CellPhyWrapper

      Public
      Wrapper for running and plotting trees using CellPhy
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • ASAP

      Public
      WGS Analysis Pipeline
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Apr 3, 2026Apr 3, 2026

    • PTATO

      Public
      PTa Analysis TOolkit
      R
      •
      MIT License
      •5•15•8•0•Updated Mar 2, 2026Mar 2, 2026

    • cloudCellphy

      Public
      A distributed framework for running Cellphy
      Nextflow
      •2•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • MutationalPatterns

      Public
      R package for extracting and visualizing mutational patterns in base substitution catalogues
      R
      •
      MIT License
      •45•9•2•0•Updated Feb 16, 2026Feb 16, 2026

    • SMuRF

      Public
      Somatic Mutations Rechecker and Filtering
      Python
      •
      MIT License
      •3•4•1•1•Updated Dec 5, 2024Dec 5, 2024

    • NF-IAP

      Public
      Illumina Analysis Pipeline in Nextflow
      Nextflow
      •
      MIT License
      •5•2•0•0•Updated Oct 8, 2024Oct 8, 2024

    • NF-SMuRF

      Public
      Somatic Mutations Rechecker and Filtering
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • PrimerDesign

      Public
      Tool to design primers on a vcf file (using primer3 software)
      C
      •
      MIT License
      •4•7•1•1•Updated May 22, 2023May 22, 2023

    • Walker

      Public
      Link germline mutations with somatic variants
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 7, 2023Apr 7, 2023

    • VAFchecker

      Public
      Python
      •0•0•0•1•Updated Dec 26, 2022Dec 26, 2022

    • ELAN_tools

      Public
      Utility scripts for elabjournal
      Python
      •1•1•0•0•Updated Aug 10, 2022Aug 10, 2022

    • Genotoxin_assay

      Public
      Data and code accompanying the research protocol: "Assessing the mutagenic impact of genotoxins in human umbilical cord-blood derived stem cells"
      R
      •1•0•0•0•Updated Apr 8, 2022Apr 8, 2022

    • MutationalPatterns_manuscript2_data_scripts

      Public
      R
      •0•0•0•0•Updated Feb 23, 2022Feb 23, 2022

    • Target_capture_tools

      Public
      Scripts to analyze targeted sequencing data
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 29, 2021Dec 29, 2021

    • Mutation_accumulation_T21

      Public
      R
      •1•0•0•0•Updated Jul 17, 2020Jul 17, 2020

    • Mutational_signature_refitting

      Public
      Scripts to perform mutational signature refitting
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 9, 2020Jun 9, 2020

    • RNASeq-NF

      Public
      RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
      Nextflow
      •8•0•0•0•Updated May 26, 2020May 26, 2020

    • GenotoxicEcoli

      Public
      R
      •5•1•0•0•Updated Apr 24, 2020Apr 24, 2020

    • IAP

      Public
      Illumina analysis pipeline
      Perl
      •
      MIT License
      •15•0•0•0•Updated Apr 2, 2020Apr 2, 2020

    • MutSigPipe

      Public
      Mutational signature selection and refitting pipeline
      R
      •2•0•0•0•Updated Sep 6, 2019Sep 6, 2019

    • INDELFI

      Public
      Script for INDEL filtering
      Perl
      •1•0•0•0•Updated Apr 25, 2019Apr 25, 2019

    • Identify_lowVAF_bulk_muts

      Public
      Identify mutations that are clonally present in a clone but subclonally present in a bulk sample
      R
      •1•0•0•0•Updated Mar 28, 2019Mar 28, 2019

    • CallableLoci_processor

      Public
      Combines CallableLoci bed files from control and experimental samples.
      Python
      •1•0•0•0•Updated Mar 28, 2019Mar 28, 2019

    • filterSomatic

      Public
      Filter SNVs or Indels based on non genotype specific quality parameters.
      Python
      •1•0•0•0•Updated Mar 28, 2019Mar 28, 2019

    • SNVFI

      Public
      Single Nucleotide Variant Filtering
      dnafilteringwgs
      dnafilteringwgssnv
      Shell
      •1•1•0•0•Updated Feb 12, 2019Feb 12, 2019

    • smMIPfil

      Public
      script for smMIP data analysis
      Perl
      •1•0•0•0•Updated Jun 1, 2018Jun 1, 2018
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