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

Bioinformatics
Nima AghaeepourGarry P Nolan

Abstract

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 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. The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder. Supplementary data are available at Bioinformatics online.

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Citations

Jun 22, 2019·Journal of Dental Research·D K GaudilliereB Gaudilliere
Apr 7, 2020·Current Protocols in Cytometry·Caroline E RoeJonathan M Irish
Jul 1, 2020·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Timothy J KeyesKara L Davis
Oct 22, 2019·European Journal of Immunology·Andrea CossarizzaArturo Zychlinsky
May 18, 2019·Communications Biology·Lukas M WeberMark D Robinson
Jan 2, 2020·Nature Reviews. Rheumatology·Felix J Hartmann, Sean C Bendall
Mar 20, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Guillaume MonneretFabienne Venet
Jan 20, 2021·Nature Immunology·Evgeny KinerUNKNOWN Immunological Genome Project Consortium
Jan 12, 2020·Communications Biology·Lukas M WeberMark D Robinson
Apr 3, 2021·Immunology and Cell Biology·Felix Md Marsh-WakefieldRoslyn A Kemp
Dec 16, 2021·Science Advances·Thanaphong PhongpreechaThomas J Montine

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