EDUCE
  • About
  • educer package
    • Tutorials
  • Setup instructions
    • Updating your operating system
    • R and RStudio
    • educer package
    • Working on a server
    • bash
    • Miniconda
    • QIIME 2
    • VPN
    • Courses
      • MICB 322
    • Workshops
      • Introduction to R and RStudio
      • Introduction to the R tidyverse
      • Reproducible research
      • Intermediate R programming
      • Statistical models in R
      • Creating web apps in R with Shiny
      • Amplicon sequence analysis
  • Videos
    • Installation instructions
    • Introduction to command line
  • Course Compiler
    • About
    • Course outline
    • Example data
    • Shiny app
  • Data Manipulator
    • About
    • Normalization methods
    • Shiny app

Amplicon sequence analysis

Workshop setup instructions

  • If working off UBC campus, ensure that myVPN is set up on your computer.

  • Prepare your computer for working on a server

  • Make sure that you have installed the latest versions of R and RStudio.

  • In RStudio, select the “Console” tab in the lower left pane and copy the following code after the prompt >

    if (!require(tidyverse)) install.packages("tidyverse")
if (!require(vegan)) install.packages("vegan")
if (!require(BiocManager)) install.packages("BiocManager")
if (!require(phyloseq)) BiocManager::install("phyloseq")
if (!require(DESeq2)) BiocManager::install("DESeq2")