index.Rmd

---
title: "Meta-Workflow"
author: "Miao YU"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
cover-image: "images/cover.png"
biblio-style: apalike
link-citations: yes
github-repo: yufree/metaworkflow
description: "This is a workflow for metabolomics studies."
always_allow_html: yes
bibliography: references.bib
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(cache = F,warning = F,message = F)
```

# Preface {.unnumbered}

```{r fig.align='center', echo=FALSE, include=identical(knitr:::pandoc_to(), 'html')}
knitr::include_graphics('images/cover.png', dpi = NA)
```

This is an online handout for mass spectrometry based metabolomics data analysis. It would cover a full reproducible metabolomics workflow for data analysis and important topics related to metabolomics. Here is a list of topics:

-   Sample collection
-   Sample pretreatment
-   Principles of metabolomics data analysis
-   Software selection
-   Batch correction
-   Annotation
-   Omics analysis
-   Exposome

This is a book written in **Bookdown**. You could contribute it by a pull request in Github. A workshop based on this book could be found [here](https://github.com/yufree/mdaw). Meanwhile, a docker image [xcmsrocker](https://hub.docker.com/r/yufree/xcmsrocker/) is available for metabolomics reproducible research.

[**R**](https://www.r-project.org/) and [**Rstudio**](https://www.rstudio.com/) are the software needed in this workflow.

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