Schloss Lab Tools for Reproducible Microbiome Research 💩

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A collection of useful functions and example code created and used by the Schloss Lab for reproducible microbiome research. Perform common tasks like read output files from mothur, tidy up your microbiome data, and format rmarkdown documents for publication. See the website for more information, documentation, and examples.


You can install the latest release from CRAN:


or the development version from GitHub with:

# install.packages("devtools")

or install from a terminal using conda or mamba:

mamba install -c conda-forge r-schtools


Check out the introductory vignette for a quick start tutorial or take a look at the reference documentation for a comprehensive list of functions.

Help & Contributing

If you have questions, create a new post in Discussions.

If you come across a bug, open an issue and include a minimal reproducible example.

If you’d like to contribute, see our guidelines here.

Code of Conduct

Please note that the schtools project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.


The schtools package is licensed under the MIT license. The logo is licensed under the CC BY-SA license.


To cite schtools in publications, use:

Sovacool KL, Lesniak N, Lucas SK, Armour CR, Schloss PD (2022). schtools: Schloss Lab Tools for Reproducible Microbiome Research. doi:10.5281/zenodo.6540686,

A BibTeX entry for LaTeX users is:

  title = {{schtools}: Schloss Lab Tools for Reproducible Microbiome Research},
  author = {Kelly L. Sovacool and Nicholas Lesniak and Sarah K. Lucas and Courtney R. Armour and Patrick D. Schloss},
  year = {2022},
  doi = {10.5281/zenodo.6540686},
  url = {},