---
title: "An introduction to the metabolomicsR"
author: 
- name: Xikun Han
package: metabolomicsR
output:
  BiocStyle::html_document:
    toc_float: true
vignette: >
  %\VignetteIndexEntry{An introduction to the metabolomicsR}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r options, include=FALSE, echo=FALSE}

library(BiocStyle)
knitr::opts_chunk$set(warning=FALSE, error=FALSE, message=FALSE)


```

<br>
<strong>`{metabolomicsR}`: Tools to process, analyze, and visualize metabolomic data.</strong>

<strong>metabolomicsR</strong> is a streamlined R package to preprocess, analyze, and visualize metabolomic data. We included a set of functions for sample and metabolite quality control, outlier detection, missing value imputation, dimensional reduction, normalization, data integration, regression analysis, annotation, and visualization of data and results. The <strong>metabolomicsR</strong> is designed to be a comprehensive R package that can be easily used by researchers with basic R programming skills. The framework designed here is also versatile and is extensible to various methods and metabolomic platforms. Here, we demonstrate the step-by-step use of the main functions from this package.

<strong>Figure:</strong> Seamless workflow to preprocess, analyze, and visualize metabolomic data in <strong>metabolomicsR</strong> <img src="../man/figures/workflow.png" align="center" width="120%" height="180%"/>

<br>

# Installation

| Type        | Command                                             |
|-------------|-----------------------------------------------------|
| Development | `remotes::install_github("XikunHan/metabolomicsR")` |

<br><br>


# Workflow

To demonstrate the package, we have presented a step-by-step tutorial at [GitHub](https://xikunhan.github.io/metabolomicsR/docs/articles/Introduction.html).
