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    12 repositories

    • CRS3123_omics_manuscript

      Public
      code to reproduce analysis and figures for CRS3123 -omics manuscript (Apgar and Lyon et al., currently in submission)
      R
      •
      MIT License
      •0•1•0•0•Updated Jun 26, 2026Jun 26, 2026

    • timelagged-mb-interactions

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 24, 2026Jun 24, 2026

    • micom-time-series

      Public
      using time series data to test micom's ability to predict growth
      Jupyter Notebook
      •0•0•0•0•Updated Jun 24, 2026Jun 24, 2026

    • DietMicrobeNet

      Public
      Creating network representation of microbial metabolism of dietary compounds
      Python
      •
      MIT License
      •0•0•2•0•Updated Jun 17, 2026Jun 17, 2026

    • AMON

      Public
      Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabo…
      bioinformaticsmicrobiomemetabolome
      bioinformaticsmicrobiomemetabolomeomics-data-integration
      Python
      •
      MIT License
      •11•26•6•0•Updated Jun 3, 2026Jun 3, 2026

    • q2-SCNIC

      Public
      A QIIME2 plugin for running SCNIC
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•4•4•0•Updated Feb 1, 2026Feb 1, 2026

    • SCNIC

      Public
      Sparse Cooccurence Network Investigation for Compositional data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•25•4•0•Updated Feb 1, 2026Feb 1, 2026

    • KEGG_parser

      Public
      KEGG Parsers, extracted and refactored
      Python
      •
      MIT License
      •0•0•2•0•Updated Jan 15, 2026Jan 15, 2026

    • knowledge-source-mappings

      Public
      R
      •1•1•0•1•Updated Mar 1, 2024Mar 1, 2024

    • seq-helper-scripts

      Public
      Helper scripts for working with sequencing data (16S, MetaG, or MetaT)
      Python
      •0•0•0•0•Updated Sep 6, 2023Sep 6, 2023

    • q2-amon

      Public
      Qiime 2 plugin for AMON
      MIT License
      •0•0•0•0•Updated Sep 30, 2020Sep 30, 2020

    • Source_of_Fecal_and_Oral_Bacteria_on_Hands

      Public
      A repository containing data, methods and results for the manuscript The Prevalence and Source of Fecal and Oral Bacteria on Infant, Child and Adult Hands.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 22, 2017Dec 22, 2017
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