EnrichmentMapApp
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BaderLab
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
In the single dataset analysis the border colour is dark red and can be confusing to people who used an older version of the app. It would be better to...
Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.2.2 to 2.12.7.1. Commits See full diff in compare view [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter...
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Issue from Uros in Emili lab I have RNAseq data and phospho data and I want to create a multi dataset EM with both results but the power in RNAseq...
Add tutorial or documentation outlining how to make the network in this publication - How to use multiple datasets and how best to visualize them. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712639/
GSEA changed the format of their files. If users try and run gsea with the data and then go through the tutorial EM won't recognize their files. This might be...
Bumps [gson](https://github.com/google/gson) from 2.8.0 to 2.8.9. Release notes Sourced from gson's releases. Gson 2.8.9 Make OSGi bundle's dependency on sun.misc optional (#1993). Deprecate Gson.excluder() exposing internal Excluder class (#1986). Prevent...
Bumps logback-core from 0.9.29 to 1.2.9. [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a...
Hard to figure out what is happening when you click on the "EnrichmentMap - show in pathway commons Functionality" in the network vs. in the heatmap. From playing around with...
Not sure if this is a possibility but similiar to what STRING does when "EnrichmentMap - show in pathway commons Functionality" is clicked bring up input panel that shows: *...
the over and under expression used to colour the nodes are specific to the query as opposed to the dataset so if a given geneset has a max expression of...