Pathway enrichment analysis of gene list

Question

[onspotproductions]

I have a list of genes generated from an expression analysis. I want to run these genes through pathway enrichment, but all of the tools I have tried seem to have incomplete databases from KEG etc. I have looked at gemini pathways as an option, but don;t have a gemini dataset.

Answer 1

[h.mon]

See the function kegg.gsets from gage package on BioConductor.

Answer 2

[spleonard1]

The R bioconductor package clusterProfiler works well for simple enrichment tests on KEGG pathways and KEGG modules (also GO if you've got that info). The vignette is pretty nice, too. Check it out https://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html

You're likely looking for the function enrichKEGG()