QUALIFIER

QUALIFIER performs quality assessment of gated flow cytometry data to detect and mitigate technical variation and outlier samples using study design and experiment-level metadata.

Key Features:

• R package integration: Integrates the flowWorkspace and QUAliFiER R packages to form a pipeline for quality assessment of gated flow cytometry data.
• FlowJo import: Uses flowWorkspace to import pre-processed and manually gated datasets from FlowJo into BioConductor.
• Statistical quality assessment: Performs extensive statistical assessments on gated cell sub-populations to monitor population statistics.
• Study-design awareness: Leverages data structure and study design to ensure consistency across staining panels, subjects, aliquots, and channels.
• Population-level checks: Implements a series of checks that comprehensively monitor population statistics for technical anomalies.
• Outlier detection: Conducts automated monitoring conditioned on experiment-level metadata to objectively identify outlier samples and mitigate technical errors affecting multiple samples over time.
• Visualization: Provides SVG-based visualization methods to explore quality assessment results from multiple perspectives.
• Customizable routines: Supports customizable quality checks and outlier detection routines tailored to specific data analysis needs.

Scientific Applications:

• Clinical trial cytometry QC: Quality control of gated flow cytometry datasets generated in clinical trials and other high-throughput studies.
• Bias detection: Identification of technical variation and biases in cell subpopulation statistics across experimental variables such as staining panels, subjects, aliquots, and channels.
• Outlier identification: Objective detection of outlier samples conditioned on experiment-level metadata for large multi-sample experiments.
• Data integrity assessment: Assessment and mitigation of technical errors affecting multiple samples over time to support reproducible downstream analysis.

Methodology:

Integrates flowWorkspace and QUAliFiER R packages; imports pre-processed and gated FlowJo datasets into BioConductor; performs statistical quality assessments and a series of checks on gated cell sub-populations; conditions automated monitoring and outlier detection on experiment-level metadata; generates SVG-based visualizations of assessment results.