OpenRefine is "a Java-based power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web."
Access a number of tutorials ranging from introductory training to advanced analysis. Begin with the "Tour of Cytoscape" and "Basic Data Visualization" tutorials.
Gephi is a visualization and exploration software for graphs and networks, allowing users to interact with the representation, manipulate the structures, shapes and colors to reveal hidden patterns.