R/Bioconductor ecosystem for microbiome bioinformatics based on (Tree)SummarizedExperiment.
Felix G.M. Ernst
Domenick J. Braccia
Hector Corrada Bravo
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)
- mia for microbiome data analysis and manipulation
- miaViz for microbiome visualization
for generating simulated microbiome data
- External packages supporting the framework
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
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