An interface in R to CellProfiler and CellProfiler Analyst databases: CellProfiler (CP) and CellProfiler Analyst(CPA) are tools for analysing image sets of cells. The software is designed to enable biologists to easily quantify phenotypes from thousands of images automatically. CellProfileR, an R package for the statistical programming environment R, enables the users of CP/CPA to easily interface their databases (mysql, sqlite, csv) with R through generic methods. This is particularly useful where more sophisticated downstream analyses are required. Convenience functions and a number of workflows are provided. Additional feature suggestions are welcome.