Raes Lab

omixer-rpm

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

GMMs

A manually curated database of human gut metabolic modules.

QMP

Quantitative Microbiome Profiling

lorepy

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

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"

raeslab-utils

covid19_respiratory_microbiome

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

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"

RLdbRDA

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

temporal_variability_microbiome_qmp

BMIS

dyspyosis

A python package to calculate the dysbiosis score in microbiome datasets

loreplotr

Logistic regression plots in R

QMP-Microbiome-CRC-confounders

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

mocat2

Latest MOCAT2 version

fgfp-gwas

Replication Cookbook for FGFP GWAS

Webservices-tester

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