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.
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:
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 index.page. 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: http://microbiome.github.com/microbiome. 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 MÃ¼ller, 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).