Hello, I'm a new (<4months) R user working in an academic lab, and trying to do some RNAseq analysis for an experiment. I am using DESeq2 to compare expression levels.
What is the best way to integrate a DESeqDataSet with TopGO or another gene ontology enrichment package?
After creating the DESeqDataSet, I would like to use a list of the top differentially expressed genes from an RNAseq run to get a list of GO terms, and then to enrich that list of GO terms to the most likely parent. Ideally, I would be able to use accessions from the same assembly the libraries were aligned to. I am working with S. aureus USA300 and an S. cerevisiae S288C variant.
Does anyone have any pointers about how to approach this best, or resources that would be helpful in this project?