Instructor: Kim Dill-McFarland (UBC/ECOSCOPE)

Title: Microbiome data manipulation and visualization in R

Target audience: anyone interested in learning R, particularly bioinformaticians and microbiologists

Course plan:

On the cluster

• 1-1:20 (Lecture): Intro to R and microbiome-relevant packages
• 1:20-1:35 (Follow-along): Downloading packages and utilizing R on a cluster
• 1:35-2:00 (Follow-along): Phylogenetic trees in R

On personal machines

• 2:00-3:00 (mixed): Data manipulation in RStudio using the tidyverse
• 3:00-4:00 (mixed): Data visualization in RStudio using phyloseq

If you would like to see specific microbiome data visualizations included in this workshop, please complete this survey and we will do our best to incorporate or provide resources toward your goals.

You can download this session’s materials from GitHub.

Duration: 3 hours

Level: beginner

Prerequisites: No prior experience is necessary but participants should install R and RStudio on their personal laptops prior to the session.

Setup:

• Cluster reservation: 4-8 cores/user for the first hour only (1-2pm)
• Cluster software: R version 3.4 or newer
• Laptop software: R and RStudio