yulab-smu / microbiotaprocessworkshop

The workshop of microbiome datasets analysis using MicrobiotaProcess

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)

  • 邮箱：输入你的邮箱

  • 账号:rstudio

  • 密码:welcome-to-bioc2020

microbiotaprocessworkshop's Issues

Taxonomy composition analysis Statistics and visualization of specific levels

Dear all,

When I use the Taxonomy composition analysis (class taxa, at the species level), I have 90% of the histogramm which is reprensented by the category "others", and the Top 30 major species did not appear in the figure. I wonder how to suppress the catergory "other" in order to see the 30 most abundant taxonomy species.

Thanks

diff_analysis error

Hello,
I used to run the command below without errors until I upgraded R version to 4.2.2. Now I get the error below when I try to run the same command on the same dataset. What could be wrong?

diff_analysis(obj= ps, classgroup = "Status",

•                  mlfun = "lda",
  

•                  filtermod = "pvalue",
  

•                  firstcomfun = "kruskal_test",
  

•                  firstalpha = 0.05,
  

•                  strictmod = TRUE,
  

•                  secondcomfun = "wilcox_test",
  

•                  subclmin = 3,
  

•                  subclwilc = TRUE,
  

•                  secondalpha = 0.01,
  

•                  lda=3)
  

Error in kruskal_test(k__Bacteria ~ Status, data = list(Row.names = c("MB1", :
could not find function "kruskal_test"

Difference in number of feature and number of taxa in diff_analysis

While running diff_analysis, the output says that original data has so many no. of feature and so many number of taxa in 7 ranks. So i want to know why features are less than taxa ?

regarding the data formatting

Hi @GuangchuangYu
I trust you are find and doing good.
I am new to microbiome and R,
I have a dataset and i am trying to analyze it.
But I don't know how to format my dataset. kindly please let me know or provide a rough data so that i can get an idea how to format the data.
Note i have got my data in excel file with OTUs in one column and the taxonomy upto species level in other columns.
Now Question 1
Do, I need to combined all the taxonomic levels into a single excel sheet.
Question 2:
How to arrange the dataset
Kindly suggest
thanks and Regards

class.xlsx
Phyllum.xlsx

regarding the installation of MetaPhlAn

Hi @ Moreno Zolfo
Hope you are fine and doing
i need some help regarding the installation of MetaPhlAn in virtual machine on windows.
secondly, if hopefully I got it installed, how to process the paired end samples
thanks and reagrds