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GSEAtopics 0.99.0

- Topic 1: Gene set resources
- Topic 1-01: Data representation of gene sets in R
- Topic 1-02: GO gene sets
- Topic 1-03: Get pathways from KEGG
- Topic 1-04: Get pathways from MSigDB
- Topic 1-05: Get pathways from Reactome
- Topic 1-06: Get gene sets from UniProt Keywords
- Topic 1-07: Get GO/KEGG gene sets for other organisms
- Topic 1-08: Generate gene sets for other organisms by mapping to orthologues
- Topic 1-09: 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
Reference

License

YEAR: 2025
COPYRIGHT HOLDER: Zuguang Gu
RESTRICTION: The code (under R/) is released under the MIT license.
             The vignettes are under the CC BY-NC-ND license.

Developed by Zuguang Gu.

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