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AutoGate specifications


Unique identifier OMICS_30180
Name AutoGate
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Mac OS, Windows
Computer skills Medium
Stability Stable
Java, Matlab
Maintained Yes




No version available


  • person_outline Leonore Herzenberg

Publication for AutoGate

AutoGate citations


QFMatch: multidimensional flow and mass cytometry samples alignment

Sci Rep
PMCID: 5818510
PMID: 29459702
DOI: 10.1038/s41598-018-21444-4

[…] The proposed workflow for analyzing all four datasets used in this manuscript consists of two steps:Preprocess the data by sequentially using utilities available in AutoGate ( to compensate the data (fluorescence flow cytometry data only), transform it with the Logicle transformation, and cluster the transformed data with DBM. See figure leg […]


Informatics Based Discovery of Disease Associated Immune Profiles

PLoS One
PMCID: 5036861
PMID: 27669154
DOI: 10.1371/journal.pone.0163305

[…] atics to handle ultra-high content cytometry data is in itself, not new, and several tools have been developed in recent years, both to enable unsupervised gating of raw cytometry data (e.g., Citrus, AutoGate) [,], and to visualize subset abundance and lineage relationships within patient populations (e.g., SPADE) []. Yet whether using manual or data-driven methods of raw cytometry data analysis, […]


Earth Mover’s Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations

PLoS One
PMCID: 4805242
PMID: 27008164
DOI: 10.1371/journal.pone.0151859

[…] The proposed workflow for analyzing all three datasets used in this manuscript consists of three steps (see ):Preprocess the data by sequentially using utilities available in AutoGate [] ( to generate compensated data, transform it with the Logicle transformation [], and cluster the transformed data with DBM []. Please see figure legends for gating se […]


Polychromatic flow cytometry in evaluating rheumatic disease patients

PMCID: 4350283
PMID: 25880288
DOI: 10.1186/s13075-015-0561-1

[…] ual template gating procedure, is capable of mitigating the sample-to-sample variation and allows for high-throughput processing of large PFC datasets []. Likewise, recently developed software called AutoGate is promising to become an automated tool for processing and analyzing PFC data [].Traditionally, the frequency (or absolute number) of each B-cell subset derived from flow cytometry analysis […]


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AutoGate institution(s)
Department of Genetics, Stanford University School of, Medicine, Stanford, CA, USA; Department of Mathematics, California Institute of Technology, Pasadena, CA, USA; Institute of Chemical Kinetics and Combustion, Novosibirsk, Russia; Department of Statistics, Stanford University, Stanford, CA, USA
AutoGate funding source(s)
Supported in part by the NIH Grant number R01AI098519.

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