Summary and Setup

Welcome to the ABACBS 2025 “Making Sense of Metagenomes” workshop!

This is a workshop developed in collaboration between researchers of Victoria and South Australia for the ABACBS 2025 conference.

Built with the Melbourne Bioinformatics fork of The Carpentries Workbench.

Contributors:

  • Calum Walsh, Peter Doherty Institute
  • Don Teng, Metabolomics South Australia
  • Feargal Ryan, Flinders University
  • Geraldine Kong, Peter Doherty Institute
  • Vini Salazar, Melbourne Bioinformatics

Please follow the steps below and install the required software before the scheduled workshop.

Datasets

Download the Franzosa_IDB_2019 RDS data file for the Multi-Omics block.

You’ll load it into R later.

RStudio Setup

We use RStudio for coding in R.

Click here and follow the instructions to install RStudio Desktop in your system.

R packages

This workshop requires two key R packages:

  • TaxSEA (for taxon-set enrichment analysis)
  • mixOmics (for multi-omics integration and DIABLO)

Please install them before the workshop following the instructions below.

R 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("TaxSEA", "mixOmics"))

If the installation completes without error, you can load the packages with:

R 

library(TaxSEA)
library(mixOmics)