DOI: 10.18129/B9.bioc.openCyto    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: 3.14

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>,Jake Wagner <jpwagner at>

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


To install this package, start R (version "4.1") and enter:

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


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


To view documentation for the version of this package installed in your system, start R and enter:



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 2.6.0
In Bioconductor since BioC 2.13 (R-3.0) (8.5 years)
License file LICENSE
Depends R (>= 3.5.0)
Imports methods, Biobase, BiocGenerics, gtools, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowStats(>= 3.99.1), flowClust(>= 3.11.4), MASS, clue, plyr, RBGL, graph, data.table, ks, RColorBrewer, lattice, rrcov, R.utils
LinkingTo Rcpp
Suggests flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto
Links To Me
Build Report  

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Source Package openCyto_2.6.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) openCyto_2.6.0.tgz
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