GateFinder: projection-based gating strategy optimization for flow and mass cytometry.
BIOINFORMATICS(2018)
Abstract
Motivation:High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.
Results:Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology.
Availability and implementation:The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder.
Supplementary information:Supplementary data are available at Bioinformatics online.
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Key words
mass cytometry,strategy optimization,flow,projection-based
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