How to do a GO enrichment analysis for large amount of data using R

Question

[mudithekanayake]

Hello, Is there any way to do a GO enrichment analysis in http://geneontology.org/ for large amount of data without doing one at a time? I have following kind of data.

                 gene
1 
ENSG00000230594 ENSG00000171155 ENSG00000224089 ENSG00000230347 ENSG00000236446 ENSG00000186471 ENSG00000101892 ENSG00000182890 ENSG00000232119 ENSG00000131721 ENSG00000101882 ENSG00000101883 ENSG00000242362 ENSG00000226685 ENSG00000125352 ENSG00000236126 ENSG00000237957 ENSG00000005893 ENSG00000125355 ENSG00000226600 ENSG00000125356 ENSG00000203989 ENSG00000226929 ENSG00000228517 ENSG00000177485 ENSG00000226023 ENSG00000236371 ENSG00000278646 ENSG00000158290
2                                                                                                                                                                                                                                                                                                                                                                                                                   ENSG00000176774 ENSG00000176746 ENSG00000232030 ENSG00000188408
3                                                                                                                                                                                                                                                                                                                                                                   ENSG00000198205 ENSG00000215174 ENSG00000165591 ENSG00000198455 ENSG00000186787 ENSG00000204271 ENSG00000147059

I need to do the analysis separately. Is there any way to do it using R? I'm new to this. I'll be grateful if someone can help me. Thank you.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[Benn]

To do GO enrichment analysis for more groups in parallel you can try clusterProfiler. I used it once to do GO enrichment analysis for 6-7 groups simultaneously.

[mudithekanayake]

Thank you very much. I'll check it out.

Answer 2

[EagleEye]

You can do any number of list parallel using GeneSCF. This tool is specifically designed to handle larger datasets in one go. You can specify the directory where the list of genes are stored (list of text files) and specify the output directory, GeneSCF takes care of the rest. Your output will be individual directories for your list with the enrichment analysis results. Note: You can also choose multiple database/repositories in a single run (Example, KEGG, Geneontology, Reactome, etc.).

Good luck.