webgestalt

This exchange is relevant for this questions https://github.com/alserglab/fgsea/issues/124 On Friday,

This change in results is due to the nature of GSEA. GSEA uses random permutations to get a

Thank you very much for the explanation and the fix. Kind regards, Klara torek, 8. april 2025 ob 19:

Hello, The KEGG database was created by querying the KEGG api using the KEGGREST R package. You can

One set of parameters that are probably creating this is the Category Parameters: Minimum number of

Hello, The algorithm for the GO terms based on the hierarchical structure of Gene Ontology. We

I forgot to mention, but in the TXT file gmt1 is the 2024 version of KEGG and gmt2 is the 2019

Hello, A common formatting issue is making sure it is tab-separated. I attached an example file to

Hello, We recently added a new parameter to the geneset API which was not updated to the R package

Hello, It seems that your GMT file is not in the correct format. There are extra spaces before each

Hello, We do have a limit for uploading files to the webserver. This is most commonly met with GMT

Could you share 10-20 IDs that are in the list? We did update the mapping files, so that could be a

Hello, For NTA with Network_Retrieval_Prioritization construction , isn't it better to take

Hello, Thank you for reporting this issue. This was not intentional and caused by a bug in the drop

Hi, In this case, the lack of overlap between my metabolites list and the Lysine Degradation Pathway

Hello, Thank you for your prompt reply, it's working fine now ! To know, I have reinstalled the R

Thank you! I'll try that. Kimberly On Tuesday, July 23, 2024 at 11:16:00 AM UTC-4 John

It works fine. Thank you very much. Best regards, Anna Στις Δευτέρα 22 Ιουλίου 2024 στις 7:14:29 μ.μ.

It is now, perfectly working. Thank you so much for your help. Best, Fernando. El lunes, 1 de julio

Hello, This may have been due to some server issues we had, depending on the time you ran the ID

We currently only support pre-ranked inputs. However, we are working on improving the visualizations

Dear Devs, The Molecular Signatures Database (MSigDB) is a popular resource for gene sets. Their

Hi John, Thanks for the detailed explanation. Best wishes, Ilian On Monday, May 13, 2024 at 10:40:53

This is a drastic difference. I previously spent some time looking into the underlying cause of the

A good starting point could be looking at Google Scholar: https://scholar.google.com/scholar?cites=

Hello, I believe this is a result of the functionality of GSEA. It doesn't necessarily care about

Hello, I am trying to run GSEA on custom database and getting the above error. Attached the

Sorry for the bug, but that should not have any affect on the data output. For those sequences, I

Sorry for the delayed response. GSEA creates random permutations to create a sample population.

terrible application