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

Closed AlexanderPico closed 1 month ago

AlexanderPico commented 1 month 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 month 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 1 month 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