GateFinder: Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
Nima Aghaeepour*, Erin F. Simonds*, David JHF Knapp, Robert V. Bruggner, Karen Sachs, Pier Federico Gherardini, Nikolay Samusik, Sean C. Bendall, Gabriela K. Fragiadakis, Brice Gaudilliere, Martin S. Angst, Connie J. Eaves, William A. Weiss, Wendy J. Fantl, Garry P. Nolan, Submitted, 2018.
High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Here we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise approaches 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, or clarify underlying biology.
Software: The GateFinder algorithm is implemented as a free and open-source package for the BioConductor suite for R. The package is accepted into BioConductor and will be made available upon publication of the accompanying article. The latest version is also available here:
- R package: Gatefinder_0.99.0.tar.gz
- Documentation: Documentation
- Quick Start Vignette: Vignette
Datasets: The datasets used in the article will be publicly available as described below (reviewer access to cytobank is possible through username: AnonymousReviewer – password: ABCD2018):
- HIV: [flowrepository]
- BMMCs: [cytobank]
- BMMCs Validation: [cytobank]
- BMMCs FCM Validation: [cytobank]
- SPADE analysis of PBMCs: [cytobank]