flowWorkspace

flowWorkspace imports and represents manually gated FlowJo flow cytometry data within the BioConductor environment to enable systematic quality assessment of gated cell populations in large studies such as clinical trials.

Key Features:

• Integration with FlowJo: Imports manually gated data from FlowJo into BioConductor to enable downstream computational analysis.
• Preservation of Analysis Settings: Preserves gating hierarchies, sample group assignments, compensation, and transformation settings from FlowJo analyses.
• Quality Assessment Pipeline (QUAliFiER): Forms a pipeline with the QUAliFiER package to perform systematic quality assessment across large datasets typical of clinical trials.
• Statistical Quality Checks: Performs statistical checks on gated cell sub-populations using study design metadata and monitors consistency across staining panels, subjects, aliquots, and channels.
• Interactive SVG-based Visualization: Provides SVG-based interactive visualization methods for exploring quality assessment results and outlier detection.

Scientific Applications:

• Clinical trial flow cytometry QC: Quality control of high-throughput flow cytometry data in clinical trials to detect instrument variation, problematic antibody staining, and reagent lot effects.
• Outlier detection and data integrity monitoring: Automated identification of outliers and systematic technical errors in gated cell population statistics to support reliable downstream analyses.

Methodology:

Manually gated FlowJo data are imported into BioConductor and processed with flowCore while preserving gating hierarchies, sample groups, compensation, and transformation settings; the QUAliFiER package then applies statistical quality assessment checks using study design metadata.