Chapter 3 Getting started

3.1 Checklist (before the workshop)

Install the following software in advance in order to avoid unnecessary delays and leaving more time for the workshop contents.

  • R (version >4.1.0)

  • RStudio; choose “Rstudio Desktop” to download the latest version. Optional but preferred. For further details, check the Rstudio home page.

  • For Windows users: Rtools; Follow the instructions to install the toolkit. This might be required to compile some of the packages required on this course.

  • Install and load the required R packages

3.2 Support and resources

For online support on installation and other matters, you can join us at:

3.3 Installing and loading the required R packages

This section shows how to install and load all required packages into the R session. Only uninstalled packages are installed.

if (!requireNamespace("BiocManager")) {

# List of packages that we need from cran and bioc 
packages <- c("ggplot2", "pheatmap", "stringr", "igraph", "ANCOMBC",
             "microbiome", "httpuv", "microbiomeDataSets", "mia", "caret", "ranger",
            "dplyr", "miaViz", "knitr", "kableExtra", "vegan", "ecodist", "biclust",
            "patchwork", "pdp", "MLmetrics", "precrec","reticulate", "MOFA2")

The following script tries to load all required packages, and if they are not available, installs them.

new.pkgs <- packages[!(packages %in% installed.packages()[, "Package"])]

if (length(new.pkgs)) {
    BiocManager::install(new.pkgs, ask=T)

sapply(packages, require, character.only = TRUE)
##            ggplot2           pheatmap            stringr             igraph 
##               TRUE               TRUE               TRUE               TRUE 
##            ANCOMBC         microbiome             httpuv microbiomeDataSets 
##               TRUE               TRUE               TRUE               TRUE 
##                mia              caret             ranger              dplyr 
##               TRUE               TRUE               TRUE               TRUE 
##             miaViz              knitr         kableExtra              vegan 
##               TRUE               TRUE               TRUE               TRUE 
##            ecodist            biclust          patchwork                pdp 
##               TRUE               TRUE               TRUE               TRUE 
##          MLmetrics            precrec         reticulate              MOFA2 
##               TRUE               TRUE               TRUE               TRUE