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@vdblab Marcel van den Brink Lab

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    17 repositories

    • dockerfiles

      Public
      Various dockerfiles for our bioinformatics pipelines
      Dockerfile
      •0•4•2•2•Updated May 29, 2026May 29, 2026

    • legacy-amplicon-pipeline

      Public
      R
      •0•0•0•1•Updated May 22, 2026May 22, 2026

    • vdblab-amplicon

      Public
      Snakemake DADA2-based 16S amplicon sequenicng workflow
      Python
      •
      MIT License
      •0•1•4•0•Updated May 19, 2026May 19, 2026

    • vdblab-shotgun

      Public
      Shotgun metagenomic sequencing processing pipeline
      Python
      •
      MIT License
      •2•1•34•1•Updated Apr 13, 2026Apr 13, 2026

    • resources

      Public
      Infrastructure for static resources used by vdblab-shotgun and vdblab-amplicon
      Python
      •1•0•3•0•Updated Mar 17, 2026Mar 17, 2026

    • vdblab-profile

      Public
      Snakemake profile for MSK's LSF-based HPC
      Python
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • FLORAL

      Public
      Fit LOg-RAtio Lasso regression for compositional covariates
      R
      •
      GNU General Public License v3.0
      •1•16•10•0•Updated Feb 8, 2026Feb 8, 2026

    • vdbR

      Public
      R
      •
      Other
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • InflaMix

      Public
      R
      •
      Other
      •3•2•0•0•Updated Mar 31, 2025Mar 31, 2025

    • FLORAL-analysis

      Public
      R code associated with the analysis results reported in FLORAL's manuscript
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 1, 2024Sep 1, 2024

    • MURINE

      Public
      Multifunction User Rodent Interface for iN-vivo Experiments
      R
      •
      Other
      •0•0•0•0•Updated Sep 26, 2023Sep 26, 2023

    • Elkrief-Colitis-FMT-2023

      Public
      R
      •0•0•0•0•Updated Sep 8, 2023Sep 8, 2023

    • Dewolf-TCR-landscape-2022

      Public template
      Supplementary data for "Tissue-specific landscape of the human T cell repertoire in graft-versus-host-disease"
      Jupyter Notebook
      •0•2•0•0•Updated Aug 9, 2023Aug 9, 2023

    • vdblab.github.io

      Public
      Creating a new repository for the vdblab GitHub Pages site
      0•0•0•0•Updated May 4, 2023May 4, 2023

    • PARADIGM

      Public
      PARADIGM - PARameters Associated with Dynamics of Gut Microbiome
      R
      •1•2•0•0•Updated Apr 11, 2023Apr 11, 2023

    • Blautia_and_GVHD

      Public
      Amplicon sequencing data accession numbers of paper: "Intestinal Blautia Is Associated with Reduced Death from Graft-versus-Host Disease" (https://pubmed.ncbi.n…
      0•0•0•0•Updated Mar 7, 2022Mar 7, 2022

    • CART_and_microbiome

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 15, 2021Nov 15, 2021
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