plateCore

plateCore extends R/Bioconductor packages flowCore and flowViz to automate gating and quantitative analysis of plate-based high-throughput flow cytometry data using negative control–based gating.

Key Features:

• Automated negative control-based gating: Implements negative control–driven automated gating to standardize gate determination across plate-based flow cytometry assays.
• Integration with R/Bioconductor: Leverages flowCore and flowViz S4 data structures and routines within Bioconductor for data handling and interoperability.
• High-throughput plate-based flow cytometry support: Handles large datasets typical of high-throughput screening workflows, including data from BD FACS CAP systems.
• Reproducible expression quantification: Produces expression values that align closely with manual FlowJo analysis, demonstrated on PBMC samples assayed for 189 human cell surface markers.

Scientific Applications:

• High-Throughput Flow Cytometry Screening: Analysis of large-scale screening experiments and datasets from instruments such as BD FACS CAP systems.
• Comparative reproducibility assessment: Automated analysis of PBMC samples assayed for 189 human cell surface markers to compare automated outputs with manual FlowJo results.

Methodology:

Uses negative control–based automated gating and leverages flowCore/flowViz S4 data structures and routines to compute expression values comparable to manual FlowJo analysis.