Question: from WGCNA to cytoscape
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gravatar for vujex
8 weeks ago by
vujex0
vujex0 wrote:

Hello

I am working with RStudio/WGCNA to make co-expression networks from RNA-seq data (40 samples and 4000 genes). I succeeded at making the similarity and adjacency matrixes now I did the following to cluster my data (and it worked)

tree <- hclust(as.dist(1 - adj.mat), method="average")

cuttreeDynamicTree: break hc dendrogram in separate modules

modules <- cutreeDynamicTree(dendro=tree, minModuleSize=15, deepSplit=TRUE)

assign colors

module_colors <- labels2colors(modules)

But I don't know how to visualise this and or export to cytoscape? I checked https://ramellose.github.io/networktutorials/wgcna.html and other posts on this forum but I didn't find anything that's working for me.

Also, does anyone know whether it's meaningful to construct a co-expression network based on rnaseq data under different conditions (e.g. drugA,B,C,D exposure, control)?

Thanks.

export cytoscape wgcna • 135 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by vujex0
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