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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

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.

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