Summary and Schedule
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
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to metagenomics |
What is metagenomics? What are the applications of metagenomics? What are the advantages of using metagenomics? What is the difference between metagenomic profiling and genome-resolved metagenomics (MAGs) |
| Duration: 00h 20m | 2. Taxon-set enrichment analysis with TaxSEA |
How can we test whether groups of related taxa (taxon sets) show
coordinated shifts between conditions? What input does TaxSEA need, and how should taxonomic IDs be formatted? How does TaxSEA extend differential abundance results using enrichment analysis? How can we interpret enriched taxon sets to understand functional, ecological, or disease-associated patterns? |
| Duration: 00h 40m | 3. Multi-omics integration with DIABLO |
How can we integrate microbiome and metabolomics data to identify shared
biological signals? What does DIABLO do, and how is it different from single-omics analyses? How do we tune a multi-omics model and choose the number of components and selected features? How do we interpret DIABLO outputs to understand discriminative multi-omics signatures? |
| Duration: 01h 40m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
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)