Pathway enrichment with gProfiler, clusterProfiler and fgsea

Learn to perform overrepresentation analysis with gProfiler and clusterProfiler, annotate differential expression using logFC and FDR thresholds, visualize with volcano plots, and prepare up/down gene lists and background for ORA.

Run an overrepresentation analysis with gProfiler using up or down gene lists, a background, chosen sources, with FDR correction and custom annotated domain scope, highlighting immune response pathways.

This lecture shows building a ranked gene list from degs using log fold change and FDR, removing duplicates, and applying clusterProfiler for functional class scoring on the ranked vector.

Combine upregulated and downregulated gProfiler results into a ggplot bubble plot, filter term size, compute gene ratio, and visualize top pathways with facet-wrapped, colored bubbles.

Create an enrichment bubble plot for clusterProfiler's ora, visualize upregulated and downregulated gene enrichment, derive the source column with gsub, and export the plot to pdf.

Plot leading edge genes tied to the interferon gamma response by converting Ensembl IDs to HGNC symbols, z-score normalizing, and visualizing an annotated heatmap to distinguish lesional skin from controls.

Learn how to ensure reproducibility in overrepresentation analysis by setting seeds, saving workspace and session info, and exporting results as heat maps and PDFs.