I have a genelist that I've analyzed in GENEmania and I would like to import this data into Cytoscape 3.0. It seems like I can only save GENEmania output as an SVG file so I cant import this into Cytoscape. I've also tried using the GENEmania app that I downloaded into Cytoscape and I can't make heads or tails of that either. Does anyone have any suggestions?
Not sure why you can't export your GeneMANIA network as text file. From the Cytoscape Web plugin on the GeneMANIA web site, I can do File > Save network as text and get a tab-delimited file.
The Cytoscape GeneMANIA app allows you to do the same thing as on the GeneMANIA web site but you have to install the network data first. Assuming you've already installed the app in Cytoscape 3.2, you go Apps > GeneMANIA > Choose another data set, check the most recent data and check 'core' (or 'all') then download data for the relevant species. Once you've installed the data, you can now query them like on the GeneMANIA web site by Apps > GeneMANIA > Search. If you installed data for multiple organisms, select the relevant one then input your query genes. Select the networks to mine and weighting scheme under Advanced options. Click on Start when ready.