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    46 repositories

    • manuals-and-policies

      Public
      2•2•0•0•Updated Nov 24, 2025Nov 24, 2025

    • isb_course_2024

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •8•5•1•10•Updated Nov 18, 2025Nov 18, 2025

    • 2025_schoch_methane

      Public
      Jasmine's work using MICOM to model methane production in the rumen microbiome (rumen metagenomes from Andersen paper)
      Jupyter Notebook
      •0•0•0•0•Updated Aug 17, 2025Aug 17, 2025

    • 2024_probiotic_engraftment

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • cdiff_invasion

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jun 18, 2025Jun 18, 2025

    • Metagenomic_Biomass_Quantification_2024

      Public
      Scripts for gut bacterial biomass analysis
      Python
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • Gibbons_Genome541_2025

      Public
      Materials, data and notebooks for GENOME 541, Spring 2025
      0•0•0•0•Updated May 12, 2025May 12, 2025

    • medi

      Public
      Metagenomic Estimation of Dietary Intake and Content.
      Nextflow
      •
      Apache License 2.0
      •6•36•13•1•Updated Apr 17, 2025Apr 17, 2025

    • pipelines

      Public
      Pipelines used in the lab.
      Nextflow
      •
      Apache License 2.0
      •3•14•0•0•Updated Mar 26, 2025Mar 26, 2025

    • 2025_aobrian_rotation

      Public
      Statin Efficacy for Varying Diets and Gut Microbes
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • medi-paper

      Public
      The accompanying paper for the MEDI method.
      HTML
      •
      Apache License 2.0
      •0•3•0•0•Updated Oct 14, 2024Oct 14, 2024

    • .github

      Public
      0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • isb_course_2023

      Public
      Materials and presentation for the 2023 ISB Microbiome course.
      analysissystems-biologysequencingmicrobiomehacktoberfestmetabolic-modelsmicrobial-ecologyqiime2pathogens16s-seq
      Jupyter Notebook
      •
      Apache License 2.0
      •13•24•0•1•Updated Sep 25, 2024Sep 25, 2024

    • JPJ_Frailty_Analysis

      Public
      Johannes JM's Analysis: Multi-omic associations between age, frailty, the gut microbiome, and the human blood plasma metabolome/proteome using the Arivale cohort.
      Jupyter Notebook
      •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • Aberrant-BMF-Cell-Reports

      Public
      Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function.
      Jupyter Notebook
      •2•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • 2023_cdiff_venturelli

      Public
      Data and code for the collab with the Venturelli lab studying C. difficile strains.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 11, 2024Jul 11, 2024

    • scfa_predictions

      Public
      Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
      Jupyter Notebook
      •3•10•0•0•Updated Jun 25, 2024Jun 25, 2024

    • IBT-and-the-Gut-Microbiome

      Public
      Repository containing the scripts, the intermediate files, and the data used in the manuscript, "Island biogeography theory and the gut microbiome: why taller people tend to harbor more diverse gut microbiomes"
      Jupyter Notebook
      •0•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • isb_course_2022

      Public
      Materials and presentation for the 2022 ISB Microbiome course.
      analysissystems-biologysequencingmicrobiomemetabolic-modelsmicrobial-ecologyqiime216s-seq
      Jupyter Notebook
      •
      Apache License 2.0
      •13•27•0•1•Updated Jun 13, 2024Jun 13, 2024

    • 2023_URTmetaanalysis

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • gapseq-docker

      Public
      A docker image for gapseq.
      Dockerfile
      •
      Apache License 2.0
      •1•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • mbtools

      Public
      R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
      R
      •
      Apache License 2.0
      •9•24•2•0•Updated Jan 24, 2024Jan 24, 2024

    • wiki

      Public
      General good-to-know stuff.
      0•1•0•0•Updated Dec 14, 2023Dec 14, 2023

    • 2021_gene_environment_interactions

      Public
      Notebooks, code and intermediate data for the Arivale gene-environment interactions.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•3•0•0•Updated Dec 4, 2023Dec 4, 2023

    • human-microbiome-time-series-growth-phase-estimation

      Public
      Analysis script for article "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes."
      HTML
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Aug 18, 2023Aug 18, 2023

    • isb_course_2021

      Public
      Materials and presentations for the 2021 ISB Virtual Microbiome Series.
      Jupyter Notebook
      •
      Apache License 2.0
      •23•27•1•2•Updated Mar 8, 2023Mar 8, 2023

    • 2022_niche_space_swegle

      Public
      A summer internship project looking at how the niche space of key microbes changes between diets
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 17, 2022Dec 17, 2022

    • isb_course_2020

      Public archive
      Materials and tutorials for the 2020 ISB Microbiome Course
      Jupyter Notebook
      •
      Other
      •28•31•0•0•Updated Nov 10, 2022Nov 10, 2022

    • 2021_data_literacy

      Public
      Data for the Data Literacy initiative
      HTML
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•0•0•Updated Oct 10, 2022Oct 10, 2022

    • 2022_infant_microbiome_arden

      Public
      Arden's summer internship project! Infant microbiome research looking into the effect of diet (breastfed, formula, and solid food) on microbiome composition and resulting metabolites.
      Apache License 2.0
      •1•0•0•0•Updated Aug 15, 2022Aug 15, 2022