<!-- README.md is generated from README.Rmd. Please edit that file -->
# MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
[](https://www.bioconductor.org/packages/MicrobiotaProcess)
[](https://github.com/YuLab-SMU/MicrobiotaProcess)
[](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html#since)
[](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html#archives)
- [**MicrobiotaProcess**](http://bioconductor.org/packages/release/bioc/html/MicrobiotaProcess.html)
defines an **MPSE** structure to better integrate both primary and
intermediate microbiome datasets.
- **MicrobiotaProcess** improves the integration and exploration of
downstream data analysis.
- **MicrobiotaProcess** provides a set of functions under a unified
tidy framework, which helps users explore related datasets more
efficiently.
- **MicrobiotaProcess** offers many visual methods to quickly render
clear and comprehensive visualizations that reveal meaningful
insights.
## Anatomy of a **MPSE**
<div class="figure" style="text-align: center">
<img src="./inst/figures/mpse.png" alt="The structure of the MPSE class." width="883" />
<p class="caption">
The structure of the MPSE class.
</p>
</div>
## Overview of the design of **MicrobiotaProcess** package
<div class="figure" style="text-align: center">
<img src="./inst/figures/mp-design.png" alt="The Overview of the design of MicrobiotaProcess package" width="1078" />
<p class="caption">
The Overview of the design of MicrobiotaProcess package
</p>
</div>
## :writing\_hand: Authors
[Shuangbin Xu](https://github.com/xiangpin) and [Guangchuang
Yu](https://guangchuangyu.github.io)
School of Basic Medical Sciences, Southern Medical University
If you use **MicrobiotaProcess** in published research. Please cite the
paper:
**Shuangbin Xu**, Li Zhan, Wenli Tang, Qianwen Wang, Zehan Dai, Land
Zhou, Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, **Guangchuang
Yu**<sup>\*</sup>. MicrobiotaProcess: A comprehensive R package for deep
mining microbiome. __*The Innovation*__. 2023, 4(2):100388. doi:
[10.1016/j.xinn.2023.100388](https://www.sciencedirect.com/science/article/pii/S2666675823000164).
- [Source code to produce Supplementary
Material](https://github.com/YuLab-SMU/MP_supplementary_file)
## :arrow\_double\_down: Installation
Get the released version from
[Bioconductor](https://bioconductor.org/packages/release/bioc/html/MicrobiotaProcess.html):
``` r
## try http:// if https:// URLs are not supported ## the url of mirror
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("MicrobiotaProcess")
```
the development version from github:
``` r
if (!requireNamespace("remotes", quietly=TRUE))
install.packages("remotes")
remotes::install_github("YuLab-SMU/MicrobiotaProcess")
```
# :book: Vignette
For more details, please refer to the [online
vignette](https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc//MicrobiotaProcess.html).
## :sparkling\_heart: Contributing
We welcome any contributions\! By participating in this project you
agree to abide by the terms outlined in the [Contributor Code of
Conduct](CONDUCT.md).
