DOI: 10.18129/B9.bioc.openCyto    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see openCyto.

Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: 3.8

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 <wjiang2 at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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 1.20.2
In Bioconductor since BioC 2.13 (R-3.0) (5.5 years)
License Artistic-2.0
Depends flowWorkspace(>= 3.17.43)
Imports methods, Biobase, BiocGenerics, gtools, flowCore(>= 1.31.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace, flowStats(>= 3.29.1), flowClust(>= 3.11.4), MASS, clue, plyr, RBGL, graph, data.table, ks, RColorBrewer, lattice, rrcov, R.utils
LinkingTo Rcpp
Suggests flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto
Depends On Me
Imports Me CytoML
Suggests Me flowCore, ggcyto
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package openCyto_1.20.2.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) openCyto_1.20.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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