Aghaeepour, Nima; Simonds, Erin F; Knapp, David JHF; Bruggner, Robert V; Sachs, Karen; Culos, Anthony; Gherardini, Pier Federico; Samusik, Nikolay; Fragiadakis, Gabriela K; Bendall, Sean C; Gaudilliere, Brice; Angst, Martin S; Eaves, Connie J; Weiss, William A; Fantl, Wendy J; Nolan, Garry P

doi:10.1093/bioinformatics/bty430

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GateFinder: projection-based gating strategy optimization for flow and mass cytometry

2018

Published Web Location

https://doi.org/10.1093/bioinformatics/bty430

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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