Guido Hooiveld

FWIW: the example code is working in my hands... ``` > library(clusterProfiler) > data(geneList, package="DOSE") > gene 2] > > kk head(kk) ID Description hsa04110 hsa04110 Cell cycle hsa04114 hsa04114...

Maybe this alternative code be of help to achieve your goal? Specifically the content of the `KEGGPATHID2NAME` slot? (which I 'extracted' as `term2name`). Both `term2gene` and `term2name` can be used...

Did you notice this message in the error that was reported: `No enrichment found in any of gene cluster, please check your input...` Please try again by setting `pvalueCutoff =...

FWIW: it is working in my hands.... see below. Please confirm you are using the current version of the packages? ``` > library(clusterProfiler) > data(geneList, package="DOSE") > gene 2] >...

@hbsycxw : what exactly is your question? That the code is not working for you? Or did you want to state it rather is working? If the former, please post...

I ran the example code you provided, and I indeed got identical results from the `enrichGO()` analysis: ``` > library(clusterProfiler) > data(geneList, package="DOSE") > gene 2] > > ego head(ego)...

What exactly is your problem? Consider opening a new issue. Be sure to provide sufficient details.

Could you please provide some reproducible code to illustrate the issue? I am asking because to me it seems everything is correct (i.e. values visualized in the `dotplot` match with...

OK, after re-reading your comment I noticed you are doing a GO-based GSEA analysis... ``` > res2 > ## 'Count' now refers to 'the number of core enriched genes' >...

In the current release version of `clusterProfiler` (i.e. v4.8.2) the function (still) is called` parse_gff()`. Yet, I noticed that in the development version of `clusterProfiler` this function had been renamed...