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This is the development version of CytoML; for the stable release version, see CytoML.

A GatingML Interface for Cross Platform Cytometry Data Sharing

Bioconductor version: Development (3.19)

Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

Author: Mike Jiang, Jake Wagner

Maintainer: Mike Jiang <mike at ozette.com>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

flowJo parser HTML R Script
How to export a GatingSet to GatingML HTML R Script
How to import Cytobank into a GatingSet HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Software
Version 2.15.2
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License AGPL-3.0-only
Depends R (>= 3.5.0)
Imports cytolib(>= 2.3.10), flowCore(>= 1.99.10), flowWorkspace(>= 4.1.8), openCyto(>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto(>= 1.11.4), yaml, stats, tibble
System Requirements xml2, GNU make, C++11
URL https://github.com/RGLab/CytoML
Bug Reports https://github.com/RGLab/CytoML/issues
See More
Suggests testthat, flowWorkspaceData, knitr, rmarkdown, parallel
Linking To cpp11, BH (>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace
Depends On Me
Imports Me
Suggests Me FlowSOM, flowWorkspace, openCyto
Links To Me
Build Report Build Report

Package Archives

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

Source Package CytoML_2.15.2.tar.gz
Windows Binary CytoML_2.15.2.zip (64-bit only)
macOS Binary (x86_64) CytoML_2.15.2.tgz
macOS Binary (arm64) CytoML_2.15.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CytoML
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoML
Bioc Package Browser https://code.bioconductor.org/browse/CytoML/
Package Short Url https://bioconductor.org/packages/CytoML/
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