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    17 repositories

    • pocpbenchmark_manuscript

      Public
      Code and manuscript for benchmarking proteins alignment tools for improved genus delineation using the Percentage Of Conserved Proteins (POCP)
      TeX
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • pocpbenchmark

      Public
      Nextflow workflow for benchmarking proteins alignment tools for improved genus delineation using the Percentage Of Conserved Proteins (POCP)
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • maldipickr_manuscript

      Public
      Worfklow for the data analysis in the maldipickr manuscript
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • hibc

      Public
      Shiny application to display data and metadata for The Human Intestinal Bacterial Collection (HiBC)
      R
      •0•0•0•0•Updated May 7, 2025May 7, 2025

    • github-repo-stats

      Public
      Statistics aggregation for Github repositories for NFDI4Microbiota KPI
      1•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • Benchmarking-shallow-Metagenomics

      Public
      Shell
      •
      MIT License
      •1•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • Protologger

      Public
      Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights
      Python
      •3•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • MiMiC2

      Public
      A workflow for the creation of synthetic communities that are functionally representative of an ecosystem.
      Python
      •
      GNU General Public License v2.0
      •2•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • genome-assembly

      Public
      A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in the Clavel Lab
      snakemakegenome-assemblysnakemake-workflowsbacterial-genomes
      Python
      •
      MIT License
      •1•3•0•0•Updated Mar 4, 2025Mar 4, 2025

    • maldipickr

      Public
      Dereplicate And Cherry-pick Mass Spectrometry Spectra
      rrstatscherry-pickmaldi-tof-msdereplicationr-packages
      R
      •
      GNU General Public License v3.0
      •1•2•4•0•Updated Feb 21, 2025Feb 21, 2025

    • consprot

      Public
      High-throughput delineation of bacterial genera
      Nextflow
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • template-dereplication-workflow

      Public
      Workflow template to dereplicate and cherry-pick mass spectrometry spectra
      R
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Nov 14, 2024Nov 14, 2024

    • miBC

      Public
      The Mouse Intestinal Bacterial Collection
      1•1•0•0•Updated Apr 24, 2024Apr 24, 2024

    • maldipickrGUI

      Public
      Workflow template to dereplicate and cherry-pick mass spectrometry spectraAn interactive interface to run reproducible workflow to dereplicate and cherry-pick mass spectrometry spectra with the 'maldipickr' package.
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 18, 2023Dec 18, 2023

    • workshop-biometadata-01

      Public
      TeX
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • SCD

      Public
      Anaerobic Single Cell Dispensing (SCD) for anaerobic cultivation of bacteria from complex samples
      0•0•0•0•Updated Nov 28, 2022Nov 28, 2022

    • MiMiC

      Public
      Minimal Microbial Consortia creation tools
      R
      •
      GNU Lesser General Public License v3.0
      •4•10•0•0•Updated Jan 28, 2022Jan 28, 2022