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 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
• phyloseq
• ggplot2
• ggtree
• vegan

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)

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  • 账号:rstudio

  • 密码:welcome-to-bioc2020