simplifyEnrichment

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Error message when running simplifyEnrichment function with clusterProfiler::GSEA() output

1

Hi. I'm trying to run simplifyEnrichment with enriched pathways from clusterProfiler GSEA function, but it gives me an error message. Below is an example with a similar analysis and the...

ftencaten

Hi @jokergoo, I came across this issue while trying to create clusters of pathways from msigdb: When clustering gene sets there some clusters whose members very low correlation, include pairwise...

adomingues

to make the order of 1, 2, 3, ... in the returned object the same as in the plot.

jokergoo

add the number of terms

jokergoo

Why the `simplifyGOFromMultipleLists(lt)` has less clusters than the components?

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Why the `simplifyGOFromMultipleLists(lt, padj_cutoff = 0.01)` has less clusters than the components? How can I maintain all the clusters of every component? And how to show the word cloud of...

danli349

Problem with clustering

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Hello everyone! I'm having trouble understanding the output of the tool, even in the example. Why the number of the clusters returned is 19, but on the heatmap are only...

GuiSeSanz

Hi, I am getting this error when using the MCL clustering Error in MCL::mcl(mat, addLoops = addLoops, allow1 = TRUE, ...)$Cluster : $ operator is invalid for atomic vectors But...

NereaSanchis

Customize simplifyGOFromMultipleLists plot

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Is it possible to change the width of the plot parts? I'd like to increase the width of the bar plots on the left and decrease the main heatmap with...

kotliary

Given that the keyword enrichment process is by far the major bottleneck, it'd be very nice to be able to parallelize it via `BiocParallel`. It seems this would be a...

j-andrews7

Hi there， I want to use "simplifyEnrichment" package in R for MacOS to visualize a clustered KEGG similarity plot but an error occur, here are my code: gene.KEGG_hyper2

sherryfan030