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README.Rmd
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README.Rmd
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---
output:
md_document:
variant: gfm
html_preview: false
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# Workshop of microbiome dataset analysis using MicrobiotaProcess
# Instructors name and contact information
- Shuangbin Xu: [email protected]
- 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: 
+ 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