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