Some of my significant DE gene lists obtained by "Limma" contain far more than 3,000 genes. I tried to use the RDavidWebService through "BACA" or "clusterProfiler" to retrieve functional annotation (e.g. KEGG). Unfortunately, I received error messages due to the size of my genelists as indicated on Davis website : "A job with more than 3000 genes to generate gene or term cluster report will not be handled by DAVID due to resource limit" ).
I am wondering what R packages or web resources would be a good alternative for "RDavidWebService".
Your advice is highly appreciated.