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R AnalyticFlow 3 is an open-source GUI for data analysis on top of R. It is designed to simplify the process of data analysis for both R experts and beginners. It is written in Java and runs on Windows, OS X and Linux. Interactive GUI modules are available to perform data analysis without writing code, or you can write R scripts if you prefer. Then you can connect these modules (or scripts) to build an “analysis flow”, which is a workflow representing the processes of data analysis. An analysis flow can be executed by simple mouse operation, which facilitates collaborative works among people with different fields of expertise. R AnalyticFlow 3 is extensible: you can easily build custom GUI modules to add functions that you need. Custom module builder is available for this purpose, which itself is a simple, user-friendly GUI to design custom modules. Any R function including your original R script can be converted to a GUI module. It also provides typical tools such as code editor, object/file browser, graphics device, help browser and R console. There are also many useful features including code completion, debugger, object-caching, auto-backup and project manager. R AnalyticFlow 3 is freely available from our website (www.ef-prime.com). The source code is licensed under LGPL, and works with other open-source libraries including JRI, JUNG and Substance.