Code, data and companion websites

Supplementary data, interactive resources and analysis code accompanying publications of the Raes Lab. Each project below has its own companion website and GitHub repository. More software and code is available on our GitHub organisation.

Browse all repositories on GitHub

Gut microbiome cohorts

Science · 2016

Population-level analysis of gut microbiome variation

Falony G, Joossens M, Vieira-Silva S, Wang J, … Raes J

Flemish Gut Flora Project: supplementary figures and tables, genus- and OTU-level abundance tables.

Website GitHub Paper

Nature Microbiology · 2020

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

Hughes DA, Bacigalupe R, Wang J, … Timpson NJ, Raes J

FGFP microbiome GWAS: figures, supplementary tables and information, replication code and the FGFP data access procedure.

Website GitHub Paper

Gut · 2016

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J

16S rRNA sequencing data, QIIME OTU tables, phylogenetic trees and metadata.

Website GitHub Paper

The ISME Journal · 2012

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

Zoetendal EG, Raes J, van den Bogert B, … Kleerebezem M

Small-intestinal metagenome and metatranscriptome assemblies: contigs, genes, proteins and reads.

Website GitHub Paper

Quantitative microbiome profiling

Nature · 2020

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Vieira-Silva S, Falony G, Belda E, … MetaCardis Consortium, Clément K, Raes J

QMP genus and gut metabolic module (GMM) abundance matrices of the MetaCardis BMIS dataset.

Website GitHub Paper

Nature Microbiology · 2019

Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses

Vieira-Silva S, Sabino J, Valles-Colomer M, … Vermeire S, Raes J

Quantitative microbiome profiling (QMP) matrix of the PSC/IBD study dataset.

Website GitHub Paper

Functional module databases

Nature Microbiology · 2016

Gut Metabolic Modules (GMMs)

Vieira-Silva S, Falony G, Darzi Y, … Raes J · Species–function relationships shape ecological properties of the human gut microbiome

Manually curated gut-specific metabolic modules with interactive metabolic maps.

Website Metabolic maps GitHub Paper

Nature Microbiology · 2019

Gut-Brain Modules (GBMs)

Valles-Colomer M, Falony G, Darzi Y, … Vieira-Silva S, Raes J · The neuroactive potential of the human gut microbiota in quality of life and depression

Manually curated modules for neuroactive compound production and degradation by gut microbes.

Website GitHub Paper

Ocean microbiome (Tara Oceans)

Science · 2015

Determinants of community structure in the global plankton interactome

Lima-Mendez G, Faust K, Henry N, … Bowler C, de Vargas C, Raes J

Supplementary tables and figures, the global plankton interaction network and an interactive network viewer.

GitHub Paper

Nature · 2016

Plankton networks driving carbon export in the oligotrophic ocean

Guidi L, Chaffron S, Bittner L, Eveillard D, … Bowler C, Gorsky G

Supplementary tables, normalized abundance matrices and the carbon-export community network viewer.

GitHub Paper

More code on GitHub. Analysis code, R and Python packages and tools developed by the Raes Lab (e.g. QMP, omixer-rpm, lorepy, dyspyosis) are available on our GitHub organisation.

github.com/raeslab