README.Rmd

---
output: 
  md_document:
    variant: gfm
html_preview: false
---

<!-- 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

```{r, echo=FALSE, results="hide", message=FALSE}
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")`
[![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** 

```{r, echo=FALSE, fig.width = 12, dpi=400, fig.align="center", fig.cap= "The structure of the MPSE class."}
knitr::include_graphics("./inst/figures/mpse.png")
```

## Overview of the design of **MicrobiotaProcess** package

```{r, echo=FALSE, fig.width = 12, dpi=400, fig.align="center", fig.cap="The Overview of the design of MicrobiotaProcess package"}
knitr::include_graphics("./inst/figures/mp-design.png")
```

## :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).