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README.Rmd
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README.Rmd
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---
output:
github_document:
html_preview: false
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# schtools <a href='http://www.schlosslab.org/schtools/'><img src='man/figures/logo.png' align="right" height="139" /></a>
Schloss Lab Tools for Reproducible Microbiome Research 💩
<!-- badges: start -->
[](https://github.com/SchlossLab/schtools/actions)
[](https://app.codecov.io/gh/SchlossLab/schtools?branch=main)
[](https://github.com/SchlossLab/schtools/blob/main/LICENSE.md)
[](https://CRAN.R-project.org/package=schtools)
[](https://anaconda.org/conda-forge/r-schtools)
[](https://zenodo.org/badge/latestdoi/8862218)
<!-- badges: end -->
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](https://mothur.org), tidy up your microbiome data,
and format rmarkdown documents for publication. See the
[website](http://www.schlosslab.org/schtools/) for more information,
documentation, and examples.
## Installation
You can install the latest release from [CRAN](https://cran.r-project.org/package=schtools):
<img src='https://cranlogs.r-pkg.org/badges/grand-total/schtools' align='right'/>
```{r, eval = FALSE}
install.packages("schtools")
```
or the development version from [GitHub](https://github.com/SchlossLab/schtools) with:
```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("SchlossLab/schtools")
```
or install from a terminal using
[conda](https://docs.conda.io/projects/conda/en/latest/index.html)
or [mamba](https://mamba.readthedocs.io/en/latest/):
<img src='https://anaconda.org/conda-forge/r-schtools/badges/downloads.svg' align='right'/>
```{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 cite_text, echo = FALSE, results = 'asis'}
> cat(format(citation('schtools'), style = 'html'))
> ```
A BibTeX entry for LaTeX users is:
```{r cite_bibtex, echo = FALSE, comment = '', results = 'asis'}
cat("```\n", format(citation('schtools'), style = 'bibtex'), "\n```")
```