R/Bioconductor ecosystem for microbiome bioinformatics based on (Tree)SummarizedExperiment.

Key developers:

Felix G.M. Ernst
Sudarshan Shetty
Tuomas Borman
Domenick J. Braccia
Ruizhu Huang
Hector Corrada Bravo
Leo Lahti

The full list of contributors varies over time, and is identified through the individual repositories. Check each individual package for acknowledgements, contact information and references. Don't hesitate to contact us for feedback, support, or feature requests.

miaverse: R/Bioconductor framework for microbiome data science

We are envisioning to rethink microbiome data science in R/Bioconductor.

This is an open source project developing R/Bioc methods, benchmarking data, and educational material for microbiome research based on the SummarizedExperiment class and its derivatives. New contributions are very welcome. The current project brings together the following key elements:


Methods (R packages)


Example case studies and workflows are now being collected in an online reference manual, Orchestrating Microbiome Analysis with R/Bioconductor manual (beta version; under preparation). Also see the individual package vignettes for details.


Join us at the following channels: The project was introduced in European Bioconductor Meeting (EuroBioC2020), and it is linked to the European COST action network on Statistical and Machine Learning Techniques in Human Microbiome Studies.

Dissemination and training material