Registration Open for Bioc2024 July 24-26


Hierarchical Gating Pipeline for flow cytometry data

Bioconductor version: Release (3.19)

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 "4.4") 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:

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 HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 2.16.1
In Bioconductor since BioC 2.13 (R-3.0) (11 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
System Requirements
See More
Suggests flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS
Linking To cpp11, BH
Depends On Me
Imports Me CytoML
Suggests Me CATALYST, flowClust, flowCore, flowStats, flowTime, flowWorkspace, ggcyto
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package openCyto_2.16.1.tar.gz
Windows Binary
macOS Binary (x86_64) openCyto_2.16.1.tgz
macOS Binary (arm64) openCyto_2.16.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive