README.Rmd

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# Workshop of microbiome dataset analysis using MicrobiotaProcess

# Instructors name and contact information

- Shuangbin Xu: xshuangbin@163.com
  - Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Supervisor: Guangchuang Yu

# Workshop description

This workshop focuses on the bioinformatics analysis of `microbiome`. Specifically, we will demonstrate how to perform downstream analysis (after OTU picking) using `MicrobiotaProcess` and `phyloseq`. 

## Pre-requisites

+ Basic knowledge of R syntax.
+ General understanding of `Amplicon` analysis or have strong interests.
+ Familiarity with some `bioconductor` objects or `S4` class.
+ A computer that runs on Unix-like system.

## How to run Docker
- Install Docker (https://www.docker.com/)
- Pull the Docker image from Docker hub:
  `docker pull xushuangbin/microbiotaprocessworkshop`
- Run the image:
  `docker run -e PASSWORD=yourpassword -p 8787:8787 xushuangbin/microbiotaprocessworkshop`
- Log in to RStudio at [http://localhost:8787](http://localhost:8787) using username `rstudio` and password `yourpassword`. For Windows users, you also need to provide your IP address, you can find it using `docker-machine ip default`.
- Inside the RStudio, run:
  `browseVignettes(package = "xushuangbin/microbiotaprocessworkshop")`
- You can click one of the links: "HTML", "source", "R code"
- In case of `The requested page was not found` error, try add 'help/' in front of the hostname in the URL (this is a known bug):
http://localhost:8787/help/library/microbiotaprocessworkshop/doc/MicrobiotaProcessWorkshop.html

## _R_ / _Bioconductor_ packages used

+ [MicrobiotaProcess](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html)
+ [phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html)
+ [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
+ [ggtree](https://www.bioconductor.org/packages/release/bioc/html/ggtree.html)
+ [vegan](https://cran.r-project.org/web/packages/vegan/index.html)

## Time outline

| Activity                           | Time |
|------------------------------------|------|
| overview of Amplicon-Seq           |  3m  |
| pipeline of Amplicon-Seq analysis  |  4m  |
| Downstream analysis                | 10m  |
|    + rarefraction curve            |      |
|    + Alpha and beta analysis       |      |
|    + Biomarker discovery           |      |
|    + etc.                          |      |
| Hands-on demonstration             | 20m  |
| Q/A section                        |  5m  |

# Workshop goals and objectives

## Learning goals

+ Understand the basic idea of microbiome.
+ Identify the commonly practiced tools used in downstream analysis of microbiome.
+ Understand the common analysis of microbiome.

## Learning objectives

+ Get familiar with the package `MicrobiotaProcess` and `phyloseq`.
+ Perform different analysis of microbiome.
+ Get familiar with the visualization of microbiome.

## Useful links

* pkgdown website that contains all workshop materials:
https://yulab-smu.top/MicrobiotaProcessWorkshop
+ some vignettes of online:
https://yulab-smu.top/treedata-book/chapter11.html#MicrobiotaProcess https://yulab-smu.top/treedata-book/related-tools.html
* GitHub Action build status badge: ![.github/workflows/basic_checks.yaml](https://github.com/YuLab-SMU/MicrobiotaProcessWorkshop/workflows/.github/workflows/basic_checks.yaml/badge.svg)
+ rstudio cloud instance
  - http://workshop.bioc.cancerdatasci.org

  - 选择：Analysis and visualization of microbiome datasets using MicrobiotaProcess(Chinese)
  - 邮箱：输入你的邮箱

  - 账号:rstudio
  - 密码:welcome-to-bioc2020