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Tools for microbiome analysis; with multiple example data sets from published studies; extending the phyloseq class. The package is in Bioconductor and aims to provide a comprehensive collection of tools and tutorials, with a particular focus on amplicon sequencing data.

Getting started

Microbiome analysis

Statistical analysis

Tutorial workflows

Tips and tricks


New examples, tutorial pages, and other contributions are welcome. The material can be freely used, modified and distributed under the Two-clause FreeBSD license. For source code, see the Github page.


Contributions are welcome:

Contibuting new tutorials or examples

We welcome new examples and tutorials to be added in this collection, and will fully acknowledge such contributions.

You can modify one of the existing examples (.html) and make a pull request. Or, you can propose a new tutorial page. The Rmarkdown source code (..html) for all tutorials is available in the Github Fork the repository, clone it, modify the tutorials, and make a pull request.


Kindly cite this work as follows: "Leo Lahti, Sudarshan Shetty et al. (2017). Tools for microbiome analysis in R. Version . URL: Check also the relevant references listed in the manual page of each function.

The package utilizes tools from a number of other R extensions, including dplyr (Wickham, Francois, Henry, and Müller, 2017), ggplot2 (Wickham, 2009), phyloseq (McMurdie and Holmes, 2013), tidyr (Wickham, 2017), vegan (Oksanen, Blanchet, Friendly, Kindt, Legendre, McGlinn, Minchin, O’Hara, Simpson, Solymos, Stevens, Szoecs, and Wagner, 2017).