<!-- 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**^\*. 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).