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benchmark_microbiome_transformations

Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"

bmis

covid19_respiratory_microbiome

Code accompanying the manuscript "Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host"

dyspyosis

A python package to calculate the dysbiosis score in microbiome datasets

enterotype-prediction-based-on-the-life-history

Machine learning classification pipe-line used for the study "Long-term life history predicts current elderly gut microbiome"

fgfp-gwas

Replication Cookbook for FGFP GWAS

gmms

A manually curated database of human gut metabolic modules.

loreplotr

Logistic regression plots in R

lorepy

A library to create lore plots (logistic regression of the prevalence of a categorical variable in function of a continuous feature)

mocat2

Latest MOCAT2 version

omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

qmp

Quantitative Microbiome Profiling

qmp-microbiome-crc-confounders

Scripts for the manuscript "Microbiome confounders and quantitative profiling challenge established microbial targets in colorectal cancer developmental stages"

raeslab-utils

rldbrda

The RaesLab's implementation of a distance based Redundancy Analysis (dbRDA)

temporal_variability_microbiome_qmp

webservices-tester

A test script to check operational status of various webservices used in our questionnaires. Triggered daily using GitHub Actions.