R/Bioconductor ecosystem for microbiome bioinformatics based on SummarizedExperiment.

Key developers:

Felix G.M. Ernst
Ruizhu Huang
Sudarshan Shetty
Tuomas Borman
Domenick C. Braccia
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.

R/Bioc microbiome ecosystem with SummarizedExperiment

We are envisioning to rethink microbiome research 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:

The project was formally 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. For further background, see