Dataset Information
GateFinder: projection-based gating strategy optimization for flow and mass cytometry.
Ontology highlight
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.
SUBMITTER: Aghaeepour N
PROVIDER: S-EPMC6247943 | biostudies-literature | 2018 Dec
REPOSITORIES: biostudies-literature
Publications
GateFinder: projection-based gating strategy optimization for flow and mass cytometry.
Bioinformatics (Oxford, England) 20181201 23
<h4>Motivation</h4>High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.<h4>Results</h4>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 ass ...[more]
