schtools

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.

Installation

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")

or install from a terminal using
conda or
mamba:

mamba install -c conda-forge r-schtools

Usage

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.

License

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

Citation

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, http://www.schlosslab.org/schtools/.

A BibTeX entry for LaTeX users is:

 @Manual{,
  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 = {http://www.schlosslab.org/schtools/},
}