Here is the place to start with R with the goal to analyze cytometry data.

Christopher Hall provides nice resources to start and improve

Lukas Weber provides simple scripts, Rtsne-example and FlowSOM-Rtsne-example, and scripts from a CyTOF-workshop-2017.

Nello Blaser provides the scripts to create the slides used in the R for cytometry course held during spring 2018 at Haukeland University Hospital. The course included setting up R, plotting in R, downloading and uploading fcs files and manual gates from and to cytobank, loading and saving fcs files, use of different clustering algorithms, tSNE, lasso regression.

Sofie Van Gassen and Helena Toddorov gave FlowSOM workshops.

In 2013, R. Brinkman presented a Flow Cytometry Data Analysis using R course, which gives an overview at that time.