# MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework \[!\[\](https://img.shields.io/badge/release%20version-1.10.2-green.svg)\](https://www.bioconductor.org/packages/MicrobiotaProcess) \[!\[\](https://img.shields.io/badge/devel%20version-1.11.4-green.svg)\](https://github.com/YuLab-SMU/MicrobiotaProcess) \[!\[Bioc\](http://www.bioconductor.org/shields/years-in-bioc/MicrobiotaProcess.svg)\](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html#since) \[!\[platform\](http://www.bioconductor.org/shields/availability/devel/MicrobiotaProcess.svg)\](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\*\*
The structure of the MPSE class.
## Overview of the design of \*\*MicrobiotaProcess\*\* package
The Overview of the design of MicrobiotaProcess package
## :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).
