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    41 repositories

    • isb_course_2024

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•6•Updated Oct 9, 2024Oct 9, 2024

    • medi-paper

      Public
      The accompanying paper for the MEDI method.
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • .github

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

    • medi

      Public
      Metagenomic Estimation of Dietary Intake and Content.
      R
      •
      Apache License 2.0
      •4•8•4•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•21•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

    • cdiff_invasion

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 13, 2024Aug 13, 2024

    • pipelines

      Public
      Pipelines used in the lab.
      Nextflow
      •
      Apache License 2.0
      •3•10•0•0•Updated Aug 7, 2024Aug 7, 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•26•0•1•Updated Jun 13, 2024Jun 13, 2024

    • 2023_URTmetaanalysis

      Public
      Jupyter Notebook
      •0•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•20•2•0•Updated Jan 24, 2024Jan 24, 2024

    • manuals-and-policies

      Public
      2•2•0•0•Updated Dec 28, 2023Dec 28, 2023

    • 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•24•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•30•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

    • 2021_microbiome_course_utils

      Public
      A small Python package used for the course.
      Python
      •
      Apache License 2.0
      •1•3•0•0•Updated Jun 28, 2022Jun 28, 2022

    • 2021_microbiome_course_data

      Public
      Additional data and cache for the ISB Virtual Microbiome Series
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated May 17, 2022May 17, 2022

    • weight_loss_2019

      Public
      Data and scripts for the weight loss project funded by the Innovator Award.
      R
      •
      Apache License 2.0
      •1•2•0•0•Updated Oct 20, 2021Oct 20, 2021

    • mmmih

      Public archive
      Materials and slides for the 3rd Microbiome Movement – Maternal & Infant Health Summit 2021.
      HTML
      •
      Other
      •0•1•0•0•Updated May 25, 2021May 25, 2021

    • american-gut-app

      Public
      Source repository for the American Gut App.
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Feb 8, 2021Feb 8, 2021