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    48 repositories

    • medi

      Public
      Metagenomic Estimation of Dietary Intake and Content.
      Nextflow
      •
      Apache License 2.0
      •8•47•1•0•Updated Aug 5, 2026Aug 5, 2026

    • 2026_Easton_VNS

      Public
      Non-invasive Vagal Nerve Stimulation as a Potential Treatment for Repetitive Blast
      R
      •0•0•0•0•Updated Jul 14, 2026Jul 14, 2026

    • 2026_Cavon_lifestyle_and_multi-omic_determinants_of_sleep_quality

      Public
      Data analysis and visualization code for "Multivariate determinants of wearable-measured sleep quality across a large observational cohort: roles of physical ac…
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•1•Updated Apr 14, 2026Apr 14, 2026

    • Gibbons_Genome541_2025

      Public
      Materials, data and notebooks for GENOME 541, Spring 2025
      0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • manuals-and-policies

      Public
      2•2•0•0•Updated Mar 23, 2026Mar 23, 2026

    • isb_course_2024

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •8•5•1•13•Updated Feb 13, 2026Feb 13, 2026

    • 2024_probiotic_engraftment

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 23, 2025Dec 23, 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

    • 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

    • pipelines

      Public
      Pipelines used in the lab.
      Nextflow
      •
      Apache License 2.0
      •3•15•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•1•0•0•Updated Mar 21, 2025Mar 21, 2025

    • medi-paper

      Public
      The accompanying paper for the MEDI method.
      HTML
      •
      Apache License 2.0
      •0•5•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-biologysequencing
      analysissystems-biologysequencingmicrobiomehacktoberfestmetabolic-modelsmicrobial-ecologyqiime2pathogens16s-seq
      Jupyter Notebook
      •
      Apache License 2.0
      •13•25•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 cohor…
      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
      •2•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 p…
      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-biologysequencing
      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
      •0•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•25•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•4•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•29•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
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