Day 2: Counts to genes and pathways


In part 2 of this workshop series, participants will use raw gene count data generated in part 1 to perform downstream analysis of RNA-seq data using R/Rstudio, including how to analyse raw count data to obtain differentially expressed genes and pathways. We will be working on Pawsey’s Nimbus Cloud platform.

Target audience

This workshop series is suitable for people who are familiar with working at command line interface and may be new to RNA-seq for differential expression analysis. The course is beginner friendly and intended for those interested in using the command line interface for their analysis. It is also suitable for those who want to learn about and use workflows.

How to navigate the web pages

Please use the Menu bar to move between lessons. We will start Day 1 with the Setup page and then naviate to the right. Each main menu header has sub-header which will be visible when you click on the main-menu, as shown below.

Course survey!

Please fill out our course survey before you leave! Help us help you! 😁


Acknowledgements are an important way for us to demonstrate the value we bring to your research. Your research outcomes are vital for ongoing funding of the Sydney Informatics Hub and national compute facilities.

Suggested acknowledgements:

The authors acknowledge bioinformatics support and advanced computing resources provided by the Sydney Informatics Hub, a Core Research Facility at the University of Sydney, Pawsey Supercomputing Research Centre, Queensland Cyberinfrastructure Foundation (QCIF) and Australia’s National Research Education Network (AARNet) enabled through the Australian BioCommons (NCRIS via Bioplatforms Australia).

All materials copyright Sydney Informatics Hub, University of Sydney