Looking for recommendations of R package for GO enrichment analysis based on gene list and a Trinotate report

Question

[BioBing]

Hi all,

I was wondering if some of you could recommend me a good R package for GO Enrichment Analysis and creating graphs of functional gene clusters?

The data I want to use in the analysis:

1) A Trinotate annotation report that includes GO-ids/terms for each annotated gene

2) A list of genes that I want to analyze (for instance all up regulated genes in a specific treatment originating from differential gene expression analysis of RNAseq data)

Thank you!

Birgitte

Answer 1

[Satyajeet Khare]

Have you tried clusterProfiler? I recently used to make compareCluster plots and gseaplot for up and down regulated genes in my analysis. Please refer to its manual here. Its a fairly straightforward to use.

[BioBing]

Thanks! I will check it out!