Guido Hooiveld

Have you seen this information: http://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html#msigdb-analysis ?

Yes, that is indeed the way to do it. Note that you can include all arguments that you could set when analyzing a single dataset. Using the included, human example...

To get any support you should provide some reproducible code and more clear questions, because to me (at least) it is unclear what you would like to achieve....

This is an interesting question, as is the thread https://github.com/YuLab-SMU/clusterProfiler/issues/283 you referred to. My thoughts: For an over-representation analysis (ORA) a contingency (2 way frequency) table is created for analysis...

I had some time available to think and read more about this... In my post above I linked to the online lesson on "RNA-seq analysis with Bioconductor". Initially I did...

@huerqiang , @GuangchuangYu : posting again as a gentle reminder; since I (we) would appreciate hearing your opinion on this. TIA.

This code is working for me. Be sure to use the latest version of `clusterProfiler`. Also, to exclude networks problems, check that the URL above is work in your browser...

In case your web traffic is monitored, I would like to point you to this post. The proposed solution may also work for you. https://stackoverflow.com/a/76684292/19054992

It has been a while that you posted this question, but since your genes are in ENSEMBL-format: why then not use the available GO annotations from ENSEMBL in combination with...

example code continued. ``` > # PART 4: perform GO ORA analysis using all 3 ontologies > # note the use of arguments TERM2GENE and TERM2NAME. Their column > #...