DOI: 10.18129/B9.bioc.openCyto  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: 3.16

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Author: Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo

Maintainer: Mike Jiang <mike at>

Citation (from within R, enter citation("openCyto")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script An Introduction to the openCyto package
HTML R Script How to use different auto gating functions
HTML R Script How to write a csv gating template
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.10.1
In Bioconductor since BioC 2.13 (R-3.0) (9.5 years)
License AGPL-3.0-only
Depends R (>= 3.5.0)
Imports methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer
LinkingTo cpp11, BH
Suggests flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, flowWorkspace, ggcyto
Links To Me
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Source Package openCyto_2.10.1.tar.gz
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