There is an increasing interest in analyzing cytometry data with R. R is not intuitive and the learning curve is not fast. But there are rewards:

  • You can easily repeat and tweak an analysis because the analysis is a script, that is a text file with commands to run and achieve the analysis. This is especially true when using R MarkDown documents that result in a HTML report.
  • Many (maybe too many now) people made their scripts and pipelines available (list).
  • Your analysis becomes compliant with FAIR principles: Findable, Accessible, Interoperable, Reusable. And transparency improves science.
  • You don’t have to learn to write scripts from zero. All you need is to be able to read code and to adjust parameters. The more you practice, the more you learn, the more you feel self confident, the more powerful package you will master.

Some R graphical user interfaces (GUIs) exist. They are typically delivered as a Shiny application that is a R code divided into 2 parts, the user interface (UI) and the server aka the processing, as classical server/client applications on the web. The UI is a web interface available in your web browser. The server is interacting with the UI and updates its query fields adding results (graphics, tables…) from computation.

Despite efforts, there is no R graphical user interface as interactive and integrated as those of companies software that are running at your computer (offline) or on the Web (online). Offline software use the power of your computer: a) memory (RAM, GB) and processor (CPU, cores, GHz) are the limiting resources for computation, b) FCS files are not leaving the computer. Online software are using a Web browser and computation are achieved in the cloud: a) memory and processor are usually not a limit, b) FCS files are sent to the cloud and results must be retrieved once computation are done. Online software usually offer nice collaborative tools.

RStudio is an integrated development environment for R. This software presents the useful views of a running analysis. This is usually the right place to start using R. There are videos for a smooth start of RStudio.