I import a network.txt file from ARACNe, which has three columns and dozens of rows. For example, Regulator Target MI Gene1 Gene2 0.X
My impression from the above file is that the edges should be directed from regulators to their targets. However, whenever I import the file, the network edges are undirected. Any ideas on how to import the file so the edges are directed? Thanks in advance for your input and time.
In general, Cytoscape doesn't actually care about direction. If you choose Regulator as your Source and Target as your target, then you can infer the direction pretty easily source-->target. Then you can easily change your visual style to put an arrow on the end of your edge and you should get what you want.