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The MSigDB KEGG sets would be a good start.
Should be stored in /data as a .RData file.
Could also store as a .csv for the purpose of testing the gene set parser code and for example purposes.
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Dear YuLab-SMU,
thanks for the great tools for data visualization.
I ran a pre-ranked GSEA search with MSigDB for Cancer Hallmarks using GSEA 4.3.2. Now I would like to use ridgeplot() to visualize…
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Validation error in PR https://github.com/cBioPortal/datahub/pull/1613
In Circle CI test server local database, the row with value `null` in `info` table, possibly from one of earlier `seedDB.sql.g…
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hi developer, thank you so much for your helpful tools.
I tried to use irGSEA to calculate the GO -BP geneset enrichment scores. But when I calculated the enrichment score as shown below:
`skin.GO.B…
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HI Chuiqin,
I met a problem like below when I run your tutorial, could you help me debug this issue? Thanks a ton!
> irGSEA.density.scatterplot(object = pbmc3k.final, method = "UCell", show.geneset …
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> pbmc3k.final
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Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed
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Currently, having a list of significant gene sets, we compute the network using the following code:
```r
gs_ovlap = computeMsigOverlap(siggs, thresh = 0.25)
gs_ovnet = computeMsigNetwork(gs_ovla…
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Hello,
I was trying to build an Autoannotate clustering from the command line using a command:
`autoannotate annotate-clusterBoosted clusterAlgorithm=MCL labelColumn=EnrichmentMap::GS_DESCR maxWord…
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Hi,
I'm using GMT files from MolSigDB for a bunch of things, and think that an auto-assignment of Gene to KEGG pathway would be useful, rather than requiring EC number in the counts file. This would …