Popcycle

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

  1. Gating: Classification of phytoplankton cell populations using a mixture of manual gating and a semi-supervized clusterting algorithm.
  2. Light scatter conversion: Convert light scattering of each particle to cell diameter ( fsc-size-calibration) and carbon content ( fsc-poc-calibration).
  3. Population data: Perform aggregate statistics along with error propagation for the different populations. The cell population identification (gated data) and diameter and carbon content (calibrated data) 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.
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François Ribalet
Principal Research Scientist

My research interests include phytoplankon ecology, oceanography and flow cytometry.

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