Schloss Lab Tools for Reproducible Microbiome Research 💩

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:

install.packages("schtools")

or the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("SchlossLab/schtools")

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.

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 package 'schtools' in publications use:

  Kelly Sovacool, Nick Lesniak and Patrick Schloss (2021). schtools:
  Schloss Lab Tools for Reproducible Microbiome Research. R package
  version 0.1.0.9000. https://github.com/SchlossLab/schtools

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {schtools: Schloss Lab Tools for Reproducible Microbiome Research},
    author = {Kelly Sovacool and Nick Lesniak and Patrick Schloss},
    year = {2021},
    note = {R package version 0.1.0.9000},
    url = {https://github.com/SchlossLab/schtools},
  }