cytoscape / cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js
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Replace example dataset for RNA-Seq Data Analysis protocol #114

Open AlexanderPico opened 2 hours ago

AlexanderPico commented 2 hours ago

I know we've gone back and forth on this, but currently the intro experience with the public dataset is very bad for this tutorial: https://cytoscape.org/cytoscape-tutorials/protocols/rna-seq-data-analysis/#/

Attached is a simplified version of the dataset that they won't have to tweak at all in Excel. It's pre-filtered for significant up and down genes and the columns are relabeled.

Otherwise the tutorial steps can be the same, but this will give a red-blue divergent gradient and more interesting experience.

rna-seq-data-cytoscape.csv

AlexanderPico commented 1 hour ago

Upload to this folder: cytoscape-tutorials/protocols/rna-seq-data-analysis/

And after the tutorial site is rebuilt it should be accessible from this link: https://cytoscape.org/cytoscape-tutorials/protocols/rna-seq-data-analysis/rna-seq-data-cytoscape.csv

khanspers commented 33 minutes ago

So the STRING query would include all genes in the new input file, up and down, correct? The resulting network would look something like this:

Screen Shot 2024-10-25 at 5 45 59 PM