The client, Precision for Medicine, contracted us to help develop a R pipeline for processing flow cytometry data. We were given a well-defined list of tasks that we successfully accomplished:

  • review data and pipeline requirements,
  • create implementation plan for pipeline,
  • implement pipeline in publicly available data following general guidelines from opencyto.org,
  • implement gating pipeline for HVTN080,
  • perform autogating of raw FCS files with OpenCyto,
  • output gated data from autogating pipeline,
  • visualize gated data using OpenCyto functions and write wrapper functions to allow for more flexibility in plotting options,
  • output patient-level data by biomarker for downstream processing, and
  • document implementation steps.