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@msysbio Lab of microbial systems biology

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    12 repositories

    • dysbiosis

      Public
      Simulations and analyses of sequencing data for healthy and dysbiotic microbial communities
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • PlasticEnz

      Public
      Python
      •0•2•0•0•Updated Feb 5, 2026Feb 5, 2026

    • microbetag

      Public
      annotating microbial co-occurrence networks
      Python
      •
      GNU General Public License v3.0
      •6•12•13•2•Updated Oct 7, 2025Oct 7, 2025

    • MGG

      Public
      Gui for Microbetag based on scNetViz
      Java
      •
      Apache License 2.0
      •6•4•4•0•Updated Aug 19, 2025Aug 19, 2025

    • microbetagApp-public

      Public
      microbetag web service
      Python
      •0•1•6•0•Updated Aug 19, 2025Aug 19, 2025

    • bacterial_growth

      Public
      a database and an interface for bacterial growth data
      pythonsqlgrowth-curves
      pythonsqlgrowth-curvesbacterial-database
      Python
      •3•2•14•1•Updated Jun 17, 2025Jun 17, 2025

    • CellScanner

      Public
      CellScanner counts microbial species in flow cytometry data of communities separately with the help of a classifier that is trained on mono-cultures.
      Python
      •
      GNU General Public License v3.0
      •1•1•6•1•Updated Apr 1, 2025Apr 1, 2025

    • PlasticDaphnia-ISMEJ

      Public
      Effects of microplastics on Daphnia-associated microbiomes in situ and in vitro
      HTML
      •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

    • BTRI_mucin_study_data

      Public
      Processed RNA-seq and fermentation data for "Starvation response strategies of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis and th…
      0•1•0•0•Updated Feb 13, 2024Feb 13, 2024

    • BTRI_mucin_study_scripts

      Public
      Scripts for "Starvation response strategies of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis and their impact on co-culture dynamic…
      MATLAB
      •0•1•0•0•Updated Feb 17, 2023Feb 17, 2023

    • .github

      Public
      msysbio-welcome
      0•2•0•0•Updated Dec 20, 2022Dec 20, 2022

    • GutMicrobes2022

      Public
      Supplementary Material for van de Velde et al. Gut Microbes 2022
      R
      •0•0•0•0•Updated Dec 20, 2022Dec 20, 2022
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