In SchlossLab/schtools: Schloss Lab Tools for Reproducible Microbiome Research

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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:

```{bash conda, eval = FALSE} mamba install -c conda-forge r-schtools

## Usage

Check out the 
[introductory vignette](http://www.schlosslab.org/schtools/articles/introduction.html) 
for a quick start tutorial or take a look at the 
[reference documentation](http://www.schlosslab.org/schtools/reference/index.html) 
for a comprehensive list of functions.

## Help & Contributing

If you have questions, create a new post in 
[Discussions](https://github.com/SchlossLab/schtools/discussions).

If you come across a bug, [open an
issue](https://github.com/SchlossLab/schtools/issues) and include a [minimal
reproducible example](https://www.tidyverse.org/help/).

If you'd like to contribute, see our guidelines
[here](http://www.schlosslab.org/schtools/CONTRIBUTING.html).

## Code of Conduct

Please note that the schtools project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## License

The schtools package is licensed under 
the [MIT license](https://github.com/SchlossLab/schtools/blob/main/LICENSE.md#mit-license).
The logo is licensed under the 
[CC BY-SA license](https://github.com/SchlossLab/schtools/blob/main/LICENSE.md#creative-commons-share-alike-license).

## Citation

To cite schtools in publications, use:

> ```r
> cat(format(citation('schtools'), style = 'html'))
> ```


A BibTeX entry for LaTeX users is:

```r
cat("```\n", format(citation('schtools'), style = 'bibtex'), "\n```")