Functional enrichment slides, HTML, PDF, Rmd

Exercises

Functional enrichment analysis of genes using topGO, roast/mroast/fry from limma, clusterProfiler package, and Fisher’s exact test, Enrichment_Genes.Rmd

More on gene set enrichment analysis using limma, https://genomicsclass.github.io/book/pages/gene_set_analysis_in_R.html

A function to perform GO/KEGG/MSigDB enrichment analysis using GOStats and Fisher’s exact test, https://github.com/mdozmorov/MDmisc/blob/master/R/gene_enrichment.R

Visualizing enriched KEGG canonical pathways with pathview, EnrichmentOverlay.Rmd

Functional enrichment of genomic regions using ChIPpeakAnno, Enrichment_Regions.Rmd

References

Ackermann, Marit, and Korbinian Strimmer. “A General Modular Framework for Gene Set Enrichment Analysis.” BMC Bioinformatics, 2009 http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-47

Nam, Dougu, and Seon-Young Kim. “Gene-Set Approach for Expression Pattern Analysis.” Briefings in Bioinformatics, 2008 http://bib.oxfordjournals.org/content/9/3/189.long

Goeman, J. J., and P. Buhlmann. “Analyzing Gene Expression Data in Terms of Gene Sets: Methodological Issues.” Bioinformatics, 2007 http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btm051