BioNERO and Cystoscope
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Hasani • 0
@8b096514
Last seen 4 days ago
United Kingdom

Is it possible to export the networks created by BioNERO onto Cystoscope?

#BioNERO BioNERO Cystoscope • 55 views
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@fabricio_almeidasilva-14890
Last seen 1 day ago
Ghent, Belgium

Hi,

Yes. Cytoscape accepts networks as "edge lists" (i.e., a 2-column table representing the genes of each edge).

You can extract the edge list for a particular module with the function get_edge_list() (see here for details, including different methods to filter spurious edges out), and then you can write the data frame to a .tsv or .txt file with the base R function write.table().

If you're doing it for multiple modules (or even all of them) and want to color nodes based on the module to which they belong, you can use the data frame genes_and_modules in the list returned by the function exp2gcn(). For instance, if your network is named my_network, you can access such data frame in my_network\$genes_and_modules.

Best,

Fabricio