what is the best gene ontology enrichment analysis package to include the pipeline
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7.9 years ago
jack ▴ 950

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?

ontology genome RNA-Seq R • 5.1k views
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7.9 years ago
dago ★ 2.7k

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

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