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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Issue with Cytoscape output file #281

Open alirosen opened 8 months ago

alirosen commented 8 months ago

Hi,

I am trying to load my network (.cys) file into Cytoscape but get this error:

Don't know how to read file:/network_CD8_Tcells/cys

I used this code to convert my network to a Cytoscape file: export_to_cytoscape(G, pos, out_file = os.path.join(work_dir, 'scenicplus/network_CD8_T_cells.cys'))

Can anyone assist with this?

redvoidling commented 8 months ago

Same Problem here!

alirosen commented 8 months ago

@redvoidling if you export the node and edge tables as .csv files you can just import them directly into Cytoscape :)