Mike Kucera comments

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                                            Mike Kucera

filtering GSEA results by NES assumes positives are in one file and negatives are in another

What is the format of the header row of your files? It looks like EM is assuming that GSEA results have 11 columns.

filtering GSEA results by NES assumes positives are in one file and negatives are in another

Hi Ruth, What is the actual problem? I just tried creating a network from a GSEA data set and I swapped the positive and negative files and it appears to...

Post analysis node size is disproportionate

It looks like in EM2 the size of a signature gene set node is constant (in fact the gene set size attribute is blank). How should it work in EM3?...

"Dark matter" - explore genes not found in any of the genesets in the context of the enrichment map

Add p-values for genes after the fact

Multiple edges for Post Analysis

Can we maybe have options: lesser - compute just lesser than edges (make all created edge color for lesser) greater - compute just greater than edges (make all created edge...

Update the read the docs tutorial to use updated GSEA data

Possibly use the GSEAtutoria_4.1 data that I have.

Update the read the docs tutorial to use updated GSEA data

Done

How to add label to bubbleset and/or to a legend?

I've done this by putting all the nodes that I want in the bubbleset into a compound node as well, and then setting the label on the compound node. With...

Improving ESM support and documentation, esp. for browsers

Released in 3.29.x

Building Enrichment Map error

Please make sure you are using the latest version of the EnrichmentMap app.