Looking for recommendations of R package for GO enrichment analysis based on gene list and a Trinotate report
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5.4 years ago
BioBing ▴ 150

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

RNA-Seq R Trinotate GO • 2.1k views
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Entering edit mode
5.4 years ago
Satyajeet Khare ★ 1.6k

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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Thanks! I will check it out!

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