I have flow cytometric data from a series of phytoplankton samples. I organized all the FCS files into flowSets using the flowCore package. My next step would be to determine compositional differences between the samples. The flowCore package offers some options for basic operations on the data, such as gating, subsetting, etc, but now I wonder if there are any more sophicticated packages for a more in-depth analysis. Any suggestions or experience shared would be highly appreciated!