Day 2 wrap up

Today, we performed differential expression and functional enrichment analysis using a gene count matrix file generated from nfcore/rnaseq (Day 1). We learnt:

  • How to perform exploratory analysis to understand the quality and properties of our data
  • How to use DESeq2 to perform differential expression analysis and check that the model was applied correctly
  • How to perform gene ontology (GO) enrichment with clusterProfiler
  • How to visualise our data and results with clusterProfiler:
    • Bar plots
    • Principal components analysis plots
    • Volcano plots
    • Heatmaps

We performed this analysis with recommended scientific practices that allow for portable and reproducible analysis including:

  • Using a singularity container with pre-installed libraries and R environment.
    • This container is on CVMFS (a filesystem), available through Pawsey Nimbus for your own analysis
  • Using Rmd to run code interactively and include commentary/documentation around the analysis

Course survey!

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

All materials copyright Sydney Informatics Hub, University of Sydney