EnrichmentMapApp
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BaderLab
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
Using FGSEA to analyze data and create "fake" GSEA results files but putting all results into one file (with both positive and negative in the same file to reduce amount...
Dear all, I'm currently analyzing snRNA-seq data, here we performed pseudobulk differential gene expression analysis (DESeq2) and are doing a GSEA using clusterProfiler afterwards. In order to get a visual...
these thresholds set a maximum for inclusion, not a minimum, right?
The `enrichmentmap build` command always creates 2 datasets when a gmt file is provided even if there is only enrichments for 1 data set. Bug was introduced by commit c2fe04c8df153aa55e9f6e3efb23ee74252df30e
When dealing with a lot of different datasets it would be good to be able to quickly group nodes from a single dataset together. Ideally we could optimize the layout...
Getting this error in the console... ``` [[1;31mERROR[m] WARNING: An illegal reflective access operation has occurred [[1;31mERROR[m] WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/Users/mkucera/.m2/repository/com/google/inject/guice/4.2.3/guice-4.2.3.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) [[1;31mERROR[m] WARNING: Please...
Provide a sorted list of pathways - Possibly as a boxplot. - Make this exportable (PDF).
Click on folder icon to build EM EM says unable to find dataset even though the directory contains 3 datasets. (Initially got an unreadable error box but that somehow resolved...
Bumps apache-karaf from 4.2.1 to 4.3.8. [](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...
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requires an absolute path which is different on the docker vs. the machine where cytoscape is running. Work around - hard code the absolute path on the hosting machine.