what is the best gene ontology enrichment analysis package to include the pipeline

Question

[jack]

I have developed a pipeline . I want to include the GO analysis also in my package. I'm looking for good R package which do GO analysis and report the result as nice plots and graph.

Does anyone have some suggestions?

[dago]

You could consider to accept the answer if you found it exhaustive.

Answer 1

[dago]

I found really nice GOstats. You can then plot the results in ggplot.

Otherwise you can take a look also at topGO, which is quite easy and intuitive, or CompGO and clusterProfiler.

The latter should also have a function to make graph directly, if I am not wrong.

I hope this helps