Microbiome Visualization with Biome-Shiny

An introductory one-day workshop seeking to provide users with the knowledge to create, analyze and visualize microbiome data. The course consists of two parts: the first part, is an introduction to, and hands-on demonstration of, the DADA2 pipeline, which will be used to process a training dataset into a file that can be analyzed through the Biome-Shiny tool. The second part uses the Biome-Shiny GUI to explore the obtained dataset's microbial community composition, as well as the alpha- and beta-diversity of the dataset, and download the results for later use.

By the end of this course, participants should be able to apply the DADA2 pipeline to process their own sequenced reads, as well as to explore their data and produce a final report using Biome-Shiny.



First Part: DADA2 Pipeline

  • Hands-on DADA2 pipeline with a training dataset
  • Assess dataset accuracy and contamination with a mock community
  • Convert the ASV table with taxonomy to biom format


Second Part: Visualization with Biome-Shiny

  • Introduction to Biome-Shiny: A Shiny R app for microbiome visualization
  • Hands-on Biome-Shiny demonstration with the biom file
  • Data filtering
  • Exploring core microbiota and community composition
  • Visualizing alpha- and beta-diversity