Both are good. Gephi for Calculation and Cytoscape for visualization
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Chose Gephi
The interactivity in Gephi and the quality of the output figures are impressive. However, the selling point was the fact that we were able to link Gephi into our pipeline using Java's interface. Other products were less customizable and lacking of the sophistication Gephi …
Compared to vis.js and d3, Gephi has a much better UI and is easier to use for anyone without a strong code background. vis.js and d3 are more flexible in terms of output and are used by Quaero for more of the ongoing reporting where Gephi is used for exploratory analysis and …
R is probably stronger from a statistics, mechanics, and customization stand-point, and has some plug-ins for graph visualization, but it can still be a bit of a black box, whereas Gephi is built around graph visualization, allowing you to really play with the data, even …
There are tools out there that can probably handle much larger datasets, however. Gephi's strength is in its ease-of-use and out-of-the box readiness. Again, there's literally no code writing required to do some pretty powerful things. Being able to open the product and get to …
Gephi is better than NodeXL. More robust and user-friendly, more options for adjusting visualizations. However, Excel is more convenient for most business analyst users and supported in most environments.
I have used RStudio and Rattle for Data Analytics and although RStudio is more powerful for cleaning and mining large sets of data, Rattle is not that efficient in graph visualization where Gephi comes out as a winner.