gibbons-lab Goto Github PK

2021_data_literacy

Data for the Data Literacy initiative

2021_gene_environment_interactions

Notebooks, code and intermediate data for the Arivale gene-environment interactions.

2021_microbiome_course_data

Additional data and cache for the ISB Virtual Microbiome Series

2021_microbiome_course_utils

A small Python package used for the course.

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.

2022_niche_space_swegle

A summer internship project looking at how the niche space of key microbes changes between diets

2023_urtmetaanalysis

american-gut-app

Source repository for the American Gut App.

american_gut

Project materials to analyze the American Gut data set.

aquaponics

Analysis code and scripts for the Aquaponics collab with Jessica Day et. al.

ccmb_workshop

Data and materials for the CCMB workshop on Cloud Computing and Microbiome Bioinformatics.

cdiff_invasion

corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

evan_rotation_notebooks

Repository for Evan Pepper's Fall 2020 Rotation

frontiers_microbiology_2018

gapseq-docker

A docker image for gapseq.

generally-healthy-cohort-bmf

Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.

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

Analysis script for article "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes."

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"

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.

medi

Metagenomic Estimation of Dietary Intake and Content.

medi-paper

The accompanying paper for the MEDI method.

micom

Python package to study microbial communities using metabolic modeling.

mmmih

Materials and slides for the 3rd Microbiome Movement – Maternal & Infant Health Summit 2021.

mouse_antibiotics

Scripts and additional data for the Mouse Antibiotics project.