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Jan 30

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Jan 30

Vasileios Zogopoulos (Bill), John Elizarraras2

Jan 29

[WebGestalt WebServer] Discrepances in results in ORA, when a single vs multiple enrichment categories are selected

Hello Vasileios, Thank you for reaching out. This is intended behavior, albeit potentially confusing.

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[WebGestalt WebServer] Discrepances in results in ORA, when a single vs multiple enrichment categories are selected

Hello Vasileios, Thank you for reaching out. This is intended behavior, albeit potentially confusing.

Jan 29

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Jan 16

Katherine Stanley, … von caleb4

Jan 10

Celltype Annotation?

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Celltype Annotation?

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Jan 10

Grace Mathew, … von caleb3

Jan 10

Query about difference in results

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Jan 10

SG Hong, John Elizarraras2

9/29/25

WebGestaltR not working

This appears to be fixed. Do you still have issues? It was likely caused by a unusually high amount

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WebGestaltR not working

This appears to be fixed. Do you still have issues? It was likely caused by a unusually high amount

9/29/25

seb...@gmail.com, … ilian atanassov6

9/19/25

noRedundant list of terms

Dear John, Thank you very much for the clarification. How do you deal with situations where the leaf

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noRedundant list of terms

Dear John, Thank you very much for the clarification. How do you deal with situations where the leaf

9/19/25

Amruta Vartak, John Elizarraras2

9/15/25

Hello, The format for the RNK file is two columns separated by a tab. The first column is the gene/

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Hello, The format for the RNK file is two columns separated by a tab. The first column is the gene/

9/15/25

8/6/25

WebGestalt not working now....

i hope it come back soon...

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WebGestalt not working now....

i hope it come back soon...

8/6/25

7/21/25

Error in Functional Database, cell type, human cell landscape

Hello community, I performed last month an over-representation analysis of human genes, using the

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Error in Functional Database, cell type, human cell landscape

Hello community, I performed last month an over-representation analysis of human genes, using the

7/21/25

ilian atanassov5

7/4/25

NES exactly 0 (zero)?

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

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NES exactly 0 (zero)?

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

7/4/25

Mferreira, … John Elizarraras3

4/25/25

Different results running GSEA on the same data

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

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Different results running GSEA on the same data

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

4/25/25

Klara Kuret, John Elizarraras4

4/9/25

how can FDR be greater than 1, webgestaltpy 0.3.1

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

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how can FDR be greater than 1, webgestaltpy 0.3.1

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

4/9/25

yuechao yang, John Elizarraras2

1/16/25

KEGG pathway database

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

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KEGG pathway database

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

1/16/25

Panagiotis, John Elizarraras3

1/16/25

Functional Enrichment Analysis

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

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Functional Enrichment Analysis

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

1/16/25

Maria Christou, … John Elizarraras7

1/14/25

GSEA results in new vs old version of Webgestalt

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

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GSEA results in new vs old version of Webgestalt

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

1/14/25

Madiha Kanwal, John Elizarraras2

1/14/25

Can't upload data

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

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Can't upload data

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

1/14/25

Isha S., John Elizarraras2

1/7/25

WiKi pathway GMT file API error

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

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WiKi pathway GMT file API error

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

1/7/25

leandro villalobos, John Elizarraras2

11/18/24

ERROR: The number of annotated IDs for all functional categories are not from 3 to 2000 for the GSEA enrichment method.

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

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ERROR: The number of annotated IDs for all functional categories are not from 3 to 2000 for the GSEA enrichment method.

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

11/18/24

Pierre Laplante, John Elizarraras2

11/18/24

"cannot upload database file" with msigdb .gmt

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

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"cannot upload database file" with msigdb .gmt

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

11/18/24

Bene G., John Elizarraras2

8/7/24

ERROR: No IDs are mapped. Please check your input.

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

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ERROR: No IDs are mapped. Please check your input.

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

8/7/24

Charline Jnnt, John Elizarraras3

8/6/24

Use of a different DB for ORA enrichment in NTA analysis

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

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Use of a different DB for ORA enrichment in NTA analysis

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

8/6/24

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