Cytoscape Nodes/Interactions Export
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3.1 years ago
mlai2567 • 0

Hi All,

Does anyone with Cytoscape experience know how I might be able to export my network data as a table of nodes and their respective interactions?

I've tried exporting as an SIF but it doesn't seem to include the specific nodes and interactions. Thanks in advance!

Cheers, Michael

Cytoscape Network Analysis • 1.6k views
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Entering edit mode
3.0 years ago
scooter ▴ 540

Hi Michael, Do you mean export a set of currently selected nodes and their interactions? As you stated, SIF will give you a table of all nodes and their partners. If you want specific nodes and their partners, what I would do is to select the nodes you want to include, select all of the first neighbors of those nodes (Select->Nodes->First neighbors of selected nodes), then create a new, subnetwork of those nodes (File->New Networks->From selected nodes and all edges). Note the "all edges" -- it may be confusing but you'll actually only get the edges that select those nodes. Now you can export that network as a SIF. Does that help?

-- scooter

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