In xiangpin/MicrobitaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

library(badger)
Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}
library(conflicted)
conflicted::conflict_prefer("filter", "dplyr")
knitr::opts_chunk$set(fig.path = "inst/figures/README-")

r badge_bioc_release("MicrobiotaProcess", "green") r badge_devel("YuLab-SMU/MicrobiotaProcess", "green")

• 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

knitr::include_graphics("./inst/figures/mpse.png")

Overview of the design of MicrobiotaProcess package

knitr::include_graphics("./inst/figures/mp-design.png")

: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.

• Source code to produce Supplementary Material

: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.

xiangpin/MicrobitaProcess documentation built on April 12, 2024, 9:03 p.m.