Repositories list

• pipelines

  Public
  Pipelines used in the lab.

  Nextflow

  •

  Apache License 2.0

  •3•10•0•0•Updated Oct 18, 2024Oct 18, 2024

• isb_course_2024

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •2•2•0•6•Updated Oct 16, 2024Oct 16, 2024

• medi-paper

  Public
  The accompanying paper for the MEDI method.

  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 14, 2024Oct 14, 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

  •5•13•6•0•Updated Oct 2, 2024Oct 2, 2024

• isb_course_2023

  Public
  Materials and presentation for the 2023 ISB Microbiome course.

  analysissystems-biologysequencing+ 7microbiomehacktoberfestmetabolic-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

• cdiff_invasion

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Aug 13, 2024Aug 13, 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

  •4•9•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-biologysequencing+ 5microbiomemetabolic-modelsmicrobial-ecologyqiime216s-seq

  Jupyter Notebook

  •

  Apache License 2.0

  •13•27•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

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  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•23•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

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  Apache License 2.0

  •23•25•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

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  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

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  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

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  Apache License 2.0

  •1•1•0•0•Updated Feb 8, 2021Feb 8, 2021