README.md

Popcycle

Popcycle is an R package that offers a reproducible approach to process, calibrate and curate flow cytometry data collected by SeaFlow.

Popcycle workflow Raw data are stored every 3 minutes in a custom binary file format (RAW data) consisting of eight 16-bit integer channels, along with metadata provided by the ship's data system (e.g., time, location, sea surface temperature, salinity, light intensity). The files are stored in day-of-year-labeled directories, each containing raw files with the associated log file.

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.

Install

In this project's directory, run the install script setup.R. This will install devtools, BiocManager, and any dependencies listed in DESCRIPTION. It will not upgrade any packages. To upgrade dependencies, manually run the install commands in setup.R in an interactive R environment making sure to set install options for upgrading or updating appropriately.

Rscript setup.R

Analysis

To get started with the analysis, go to the wiki



armbrustlab/popcycle documentation built on Aug. 8, 2020, 1:08 a.m.