Training and learning materials of gene set enrichment analysis.

Basic

Topics

Topic 1: gene set resources

• Topic 1-00: Representation of gene sets in R
• Topic 1-01: GO gene sets
• Topic 1-02: Get pathways from KEGG
• Topic 1-03: Get pathways from MSigDB
• Topic 1-04: Get pathways from Reactome
• Topic 1-05: Get gene sets from UniProt Keywords
• Topic 1-06: Get GO/KEGG gene sets for other organisms
• Topic 1-07: Generate gene sets for other organisms by mapping to orthologues
• Topic 1-08: Gene ID conversion

Topic 2: ORA and GSEA

• Topic 2-01: ORA on a single gene set
• Topic 2-02: Implement ORA from scratch
• Topic 2-03: Implement GSEA from scratch
• Topic 2-04: fgsea
• Topic 2-05: Compare ORA and GSEA

Topic 3: Application in genomics

• Topic 3-01: Implement the GREAT method
• Topic 3-02: Online GREAT analysis
• Topic 3-03: Local GREAT analysis

Topic 4: Topology-based

• Topic 4-01: Centrality-based pathway enrichment analysis

Topic 5: Single-sample GSEA

• Topic 5-01: Single-sample GSEA

Topic 6: Similarity, clustering and summarization

• Topic 6-01: Similarities of terms
• Topic 6-02: Cluster and summarize

Topic 7: Visualization

• Topic 7-01: Visualization

Topic 8: GSEA framework

• Topic 8-01: GSEA framework