MicrobiotaProcess
MicrobiotaProcess copied to clipboard
:microbe: A comprehensive R package for deep mining microbiome
MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
- MicrobiotaProcess 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.](https://github.com/YuLab-SMU/MicrobiotaProcess/raw/master/inst/figures/mpse.png)
The structure of the MPSE class.
Overview of the design of MicrobiotaProcess package
![The Overview of the design of MicrobiotaProcess package](https://github.com/YuLab-SMU/MicrobiotaProcess/raw/master/inst/figures/mp-design.png)
The Overview of the design of MicrobiotaProcess package
:writing_hand: Authors
Shuangbin Xu and Guangchuang Yu
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.
:arrow_double_down: Installation
Get the released version from Bioconductor:
## 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:
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.
: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.