This workshop is available for academic staff and HDR students of the ANU Shine-Dalgarno Centre for RNA Innovation and John Curtin School of Medical Research.

Workshop dates & times

This workshop runs over two afternoons from 1:00pm - 5:00pm (AEST), Monday 3rd August and Tuesday 4th August, 2026.

About the workshop

A Carpentries-style workshop equipping participants with the core skills needed to analyse RNA sequencing (RNA-seq) data using the Bioconductor ecosystem in R. RNA-seq has transformed genomics research by enabling detailed measurement of gene expression across conditions, tissues and timepoints. The workshop covers the full downstream analysis workflow: from importing and annotating quantified count data through to exploratory analysis, quality control, differential expression testing and gene set enrichment analysis. The emphasis throughout is on building a reproducible, well-documented analysis in R.

Learning Objectives

By the end of this workshop, participants will be able to:

Describe the key steps of an RNA-seq experiment and the analytical decisions that affect downstream processing.

Set up a well-organised RStudio project for an RNA-seq analysis.

Import and annotate quantified RNA-seq count data into R using Bioconductor data structures.

Perform exploratory analysis and quality control to detect problems in an RNA-seq dataset.

Conduct differential expression analysis using DESeq2, including size factor estimation, dispersion estimation and statistical testing.

Interpret and visualise differential expression results including MA plots, volcano plots and heatmaps.

Understand and construct design matrices for more complex experimental designs.

Perform gene set enrichment analysis using over-representation analysis and interpret the results.

Identify appropriate next steps for further RNA-seq analysis depending on the research question.

Other workshops in this series:

Data Analysis with R for Genomics (ANU JCSMR)

Single-cell RNA-Seq Analysis Using R (ANU JCSMR)

Spatial Transcriptomics (ANU JCSMR)

FAQs

What should I bring into the event?

This is an online workshop, so you will need to provide your own computer and have access to a reliable internet connection sufficient for video conferencing. A second monitor is highly recommended.

What prior experience do I need?

Prior experience with R and RStudio is required. Participants should also be familiar with Bioconductor, statistical hypothesis testing and the biology of gene expression and RNA-seq. Those new to R should first complete 'R for Reproducible Scientific Analysis' or 'Data Analysis with R for Genomics'. R, RStudio and a suite of Bioconductor packages must be installed before the first session. Detailed installation instructions will be provided on registration. A full-function computer (Windows, Mac or Linux) is required. Chromebooks and tablets are not suitable. A second monitor is strongly recommended. A reliable internet connection suitable for video conferencing is essential.

Who should attend?

Researchers working with RNA-seq data who want to conduct and understand the downstream statistical analysis workflow using R and Bioconductor, rather than relying on pre-built pipelines.

How can I contact the organiser with any questions?

You can email training@qcif.edu.au.

Contact the host of RNA-Seq Analysis with R (ANU JCSMR)

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