Popcycle is an R package that offers a reproducible approach to process, calibrate and curate flow cytometry data measured by SeaFlow.
The software package performs 3 key analyses
Gating: Classification of phytoplankton cell populations using a mixture of manual gating and a semi-supervized clusterting algorithm.
Light scatter conversion: Convert light scattering of each particle to cell diameter ( fsc-size-calibration) and carbon content ( fsc-poc-calibration).
Population data: Perform aggregate statistics along with error propagation for the different populations. The cell population identification (
gateddata) and diameter and carbon content (
calibrateddata) of each OPP are saved as separate text files with a similar file structure as the RAW data. The metadata, gating scheme, and aggregated statistics for each step are saved to a SQL database using SQLite3.