RNA-Seq Analysis with R (ANU JCSMR)

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.