Gibbons Lab
The Gibbons Lab -- Microbes + Ecology + Medicine @ the Institute for Systems Biology.
Seattle, WA
Pinned Repositories
american-gut-app
Source repository for the American Gut App.
isb_course_2020
Materials and tutorials for the 2020 ISB Microbiome Course
isb_course_2021
Materials and presentations for the 2021 ISB Virtual Microbiome Series.
isb_course_2022
Materials and presentation for the 2022 ISB Microbiome course.
isb_course_2023
Materials and presentation for the 2023 ISB Microbiome course.
manuals-and-policies
mbtools
R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
pipelines
Pipelines used in the lab.
scfa_predictions
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
wiki
General good-to-know stuff.
Gibbons Lab's Repositories
Gibbons-Lab/isb_course_2020
Materials and tutorials for the 2020 ISB Microbiome Course
Gibbons-Lab/isb_course_2022
Materials and presentation for the 2022 ISB Microbiome course.
Gibbons-Lab/isb_course_2021
Materials and presentations for the 2021 ISB Virtual Microbiome Series.
Gibbons-Lab/isb_course_2023
Materials and presentation for the 2023 ISB Microbiome course.
Gibbons-Lab/mbtools
R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
Gibbons-Lab/pipelines
Pipelines used in the lab.
Gibbons-Lab/scfa_predictions
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
Gibbons-Lab/medi
Metagenomic Estimation of Dietary Intake and Content.
Gibbons-Lab/2021_gene_environment_interactions
Notebooks, code and intermediate data for the Arivale gene-environment interactions.
Gibbons-Lab/2021_microbiome_course_utils
A small Python package used for the course.
Gibbons-Lab/human-microbiome-time-series-growth-phase-estimation
Analysis script for article "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes."
Gibbons-Lab/manuals-and-policies
Gibbons-Lab/weight_loss_2019
Data and scripts for the weight loss project funded by the Innovator Award.
Gibbons-Lab/2021_data_literacy
Data for the Data Literacy initiative
Gibbons-Lab/american-gut-app
Source repository for the American Gut App.
Gibbons-Lab/cdiff_invasion
Gibbons-Lab/mmmih
Materials and slides for the 3rd Microbiome Movement – Maternal & Infant Health Summit 2021.
Gibbons-Lab/wiki
General good-to-know stuff.
Gibbons-Lab/Aberrant-BMF-Cell-Reports
Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function.
Gibbons-Lab/JPJ_Frailty_Analysis
Johannes JM's Analysis: Multi-omic associations between age, frailty, the gut microbiome, and the human blood plasma metabolome/proteome using the Arivale cohort.
Gibbons-Lab/.github
Gibbons-Lab/2021_microbiome_course_data
Additional data and cache for the ISB Virtual Microbiome Series
Gibbons-Lab/2022_infant_microbiome_arden
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.
Gibbons-Lab/2022_niche_space_swegle
A summer internship project looking at how the niche space of key microbes changes between diets
Gibbons-Lab/2023_cdiff_venturelli
Data and code for the collab with the Venturelli lab studying C. difficile strains.
Gibbons-Lab/2023_URTmetaanalysis
Gibbons-Lab/gapseq-docker
A docker image for gapseq.
Gibbons-Lab/IBT-and-the-Gut-Microbiome
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"
Gibbons-Lab/isb_course_2024
Gibbons-Lab/medi-paper
The accompanying paper for the MEDI method.