This R notebook demonstrates differential expression and functional enrichment analyses in a case control analysis. It was developed for the 2023 Introduction to RNAseq workshop. See the case study explainer for more details.
For materials accompanying this notebook, please see Day 2 the training materials for our Introduction to RNAseq workshop. A copy of the count matrix used in the workshop are also included in this repository in the data/ directory. If you'd like to run it locally, you can execute it with our RStudio for RNAseq container which has all required packages preinstalled.
To run this notebook in Gitpod, click the button below. It will take a few minutes to load in your browser.
This will open a remote Gitpod workspace with the notebook preloaded and all packages preinstalled. Gitpod is a free online IDE that allows you to run code in the cloud. The workspace will be available for free for 50 hours after you click the button. It will time out after 20 minutes of inactivity.
Once your Gitpod workspace is set up, it will open a VScode window with the files in the repository in your browser. Navigate to the Setup RStudio
The Sydney Informatics Hub is an official node of the Australian BioCommons, and has worked in partnership with National Computational Infrastructure, Pawsey Supercomputing Research Centre, and AARNet to create command-line resources that make bioinformatics more accessible for life scientists.
Acknowledgements (and co-authorship, where appropriate) 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. We suggest including the following acknowledgement in any publications that follow from this work:
"The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia".