Knight Lab Analyses

multiomic-cooccurrences

mycobiome

Pan-cancer mycobiome atlas

birdman-analyses

uc-severity-multiomics

qemistree-analyses

Analyses of metabolomics data using q2-qemistree

BayesTime-analyses

analysis code for BayeTime manuscript on simulations and microbiome applications

bloom-analyses

circadian-ihc

Circadian Experiments - Microbiome, Metabolome

evident-analyses

faiths-pd-benchmarking

imsms-ml

Data exploration and analysis scripts for the machine learning analysis of the iMSMS collaboration.

umap-microbiome-benchmarking

CR-2021

empress-analyses

Analyses, figures, and artifacts for Empress.

greengenes2

mfpca-analyses

code of simulations and real data applications for MFPCA manuscript

nutrition-gut-microbiota-mumbai

anaerobic-digesters

dynamics

Analysis of Multiple Circadian/Longitudinal Datasets

longitudinal-osa

Longitudinal OSA Experiments - Lesion, Microbiome, Metabolome

marmoset-diet-change

Shotgun metagenomic analysis of laboratory-house common marmoset breeding colony that switched from pelleted to gel diet

regression-benchmarking

SAF-PP-JPL

16S analysis for assessment of the NASA Standard Spore Assay in Predicting Bacterial Populations of a Mars Mission Assembly Facility

Saliva_quantification_study

seeding-study

Restoration of the microbiome trajectory by vaginal seeding of C-section born infants

stability-analyses

code for simulation studies and experimental microbiome data applications in Stability manuscript

stein-schizophrenia

unifrac-colab-notebooks

Notebooks for use on Google Colabs

version-testing-fastp-minimap2

version-testing for fastp-minimap2

vitamin-d

notebooks for MrOS Vitamin D manuscript