Package: openCyto 2.25.0

Mike Jiang

openCyto: Hierarchical Gating Pipeline for flow cytometry data

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

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

openCyto_2.25.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
openCyto/json (API)
NEWS

# Install 'openCyto' in R:
install.packages('openCyto', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:openCyto-2.25.0(bioc 3.24)openCyto-2.24.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologyflowcytometrydataimportpreprocessingdatarepresentationcpp

8.12 score 1 packages 472 scripts 1.6k downloads 11 mentions 54 exports 66 dependencies

Last updated from:cd43fd159f. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR204
linux-devel-arm64WARNING290
linux-devel-x86_64WARNING325
source / vignettesOK319
linux-release-arm64WARNING266
linux-release-x86_64WARNING317
macos-release-arm64WARNING225
macos-release-x86_64WARNING373
macos-oldrel-arm64WARNING256
macos-oldrel-x86_64WARNING319
windows-develWARNING233
windows-releaseWARNING291
windows-oldrelWARNING256
wasm-releaseOK166

Exports:add_popadd_pop_initCytoExploreR_.argDeparserCytoExploreR_.preprocess_csvCytoExploreR_.preprocess_rowdelete.helperGatesfast_rlmflowClust.1dflowClust.2dgate_flowclust_1dgate_flowClust_1dgate_flowclust_2dgate_flowClust_2dgate_mindensitygate_mindensity2gate_quad_sequentialgate_quad_tmixgate_quantilegatinggatingTemplategenerate_gate_templateget.helperGatesgetChildrengetGategetNodesgetParentgh_generate_templategs_add_gating_methodgs_add_gating_method_initgs_remove_gating_methodgt_delete_helpergatesgt_gatinggt_get_childrengt_get_gategt_get_helpergatesgt_get_nodesgt_get_parentgt_list_methodsgt_toggle_helpergateslistgtMethodsmindensitymindensity2plotprior_flowclustprior_flowClustquadGate.seqquadGate.tmixquantileGateregister_pluginsregisterPluginsremove_popshowtemplateGentoggle.helperGates

Dependencies:abindBHBiobaseBiocGenericsbiocmakeclicpp11cytolibdata.tableDelayedArraydeldirdir.expirydplyrfarverfilelockflowClustflowCoreflowVizflowWorkspacegenericsggplot2gluegraphgtablehexbinIDPmiscinterpIRangesisobandjpegKernSmoothlabelinglatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsncdfFlowpillarpkgconfigpngR6RBGLRColorBrewerRcppRcppEigenRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsS7scalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVector

An Introduction to the openCyto package

Rendered fromopenCytoVignette.Rmdusingknitron May 30 2026.

Last update: 2025-03-26
Started: 2014-02-05

OpenCyto: How to use different auto gating functions

Mike Jiang

Rendered fromHowToAutoGating.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-26
Started: 2016-06-02

How to write a csv gating template

Rendered fromHowToWriteCSVTemplate.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-26
Started: 2014-03-20

Readme and manuals

Help Manual

Help pageTopics
convert a gatingTemplate object to a data.tableas.data.table as.data.table.gatingTemplate
A class to represent a boolean gating method.boolMethod-class
get gating method dimensionsdims,gtMethod-method
A class to represent a dummy gating method that does nothing but serves as reference to be refered by other populationdummyMethod-class
robust linear model using an M estimatorfast_rlm
constuctor for 'fcEllipsoidGate'fcEllipsoidGate
a concrete class that reprents the ellipsoidGate generated by flowClustfcEllipsoidGate-class
a virtual class that represents the gating result generated by flowClust gating functionfcFilter-class
constuctor for 'fcFilterList'fcFilterList
a class that extends 'filterList' class.fcFilterList-class
constuctor for 'fcPolygonGate'fcPolygonGate
a concrete class that reprents the polygonGate generated by flowClustfcPolygonGate-class
constuctor for 'fcRectangleGate'fcRectangleGate
a concrete class that reprents the rectangleGate generated by flowClustfcRectangleGate-class
constructor of 'fcTree'fcTree
A class to represent a flowClust tree.fcTree-class
Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.flowClust.1d gate_flowClust_1d gate_flowclust_1d
Automatic identification of a population of interest via flowClust based on two markersflowClust.2d gate_flowClust_2d gate_flowclust_2d
Determines a cutpoint as the minimum point of a kernel density estimate between two peaksgate_mindensity mindensity
An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks.gate_mindensity2 mindensity2
sequential quadrant gating functiongate_quad_sequential quadGate.seq
quadGate based on flowClust::tmixFilergate_quad_tmix quadGate.tmix
Determine the cutpoint by the events quantile.gate_quantile quantileGate
Creates a singlet polygon gate using the prediction bands from a robust linear modelgate_singlet
a class storing the gating method and population information in a graphNEL objectgatingTemplate gatingTemplate,character-method gatingTemplate,data.table-method gatingTemplate-class
Store gates from a GatingSet in a gatingTemplate for templated gatinggenerate_gate_template
get gates saved in 'fcTree'getGate,fcTree,character-method
get nodes from 'fcTree'getNodes,fcTree-method
generate a partially complete csv template from the existing gating hierarchygh_generate_template templateGen
get the grouping variable for the gating methodgroupBy,gtMethod-method
apply a gating method to the 'GatingSet'add_pop gs_add_gating_method
Clear history of 'gs_add_gating_method' calls for a given 'GatingSet' or 'GatingSetList'add_pop_init gs_add_gating_method_init
Reverse the action of gating methods applied via 'gs_add_gating_method'gs_remove_gating_method remove_pop
Applies a gatingTemplate to a GatingSet.gating gating,gatingTemplate,GatingSet-method gt_gating gt_gating,gatingTemplate,GatingSet-method gt_gating.gatingTemplate
get children nodesgetChildren getChildren,gatingTemplate,character-method gt_get_children
get gating method from the nodegetGate,gatingTemplate,character-method gt_get_gate
get nodes from gatingTemplate objectgetNodes getNodes,gatingTemplate-method gt_get_nodes
get parent nodesgetParent getParent,gatingTemplate,character-method gt_get_parent
Print a list of the registered gating methodsgt_list_methods listgtMethods
toggle/delete the hidden flag of the helper gatesdelete.helperGates get.helperGates gt_delete_helpergates gt_get_helpergates gt_toggle_helpergates toggle.helperGates
A class to represent a gating method.gtMethod gtMethod-class
A class to represent a cell population that will be generated by a gating method.gtPopulation-class
A class representing a group of cell populations.gtSubsets-class
get the flag that determines whether gating method is applied on collapsed dataisCollapse,gtMethod-method
get gating method namenames,gtMethod-method
get population namenames,gtPopulation-method
the class that carries event indices as wellocRectangleGate-class
constructor for ocRectRefGateocRectRefGate
special gate type that mix the rectangleGate with boolean gateocRectRefGate-class
Hierarchical Gating Pipeline for flow cytometry dataopenCyto-package openCyto
Deprecated functions in package 'openCyto'.openCyto-deprecated
Some global options for openCyto See examples for the meaning of these options and how to get/set them.openCyto.options
get parameters of the gating method/functionparameters,gtMethod-method
plot a 'fcFilterList'plot,fcFilterList,ANY-method
plot the flowClust gating resultsplot,fcTree,character-method
plot the gating schemeplot,gatingTemplate,ANY-method plot,gatingTemplate,character-method plot,gatingTemplate,missing-method plot,gatingTemplate-method
A class to represent a polyFunctions gating method.polyFunctions-class
bypass the default flowWorkspace:::.addGatepop_add.ocRectangleGate pop_add.ocRectRefGate
get posteriors from a 'fcFilter' objectposteriors,fcFilter,ANY-method posteriors,fcFilter,character-method
A class to represent a preprocessing method.ppMethod ppMethod-class
get preprocessing method from the nodeppMethod,gatingTemplate,character-method
apply a ppMethod to the 'GatingSet'preprocessing,ppMethod,GatingSet-method
Elicits data-driven priors from a flowSet object for specified channelsprior_flowClust prior_flowclust
get priors from a 'fcFilter' objectpriors,fcFilter,ANY-method priors,fcFilter,character-method
A class to represent a reference gating method.refGate-class
Register a gating or preprocessing function with OpenCytoregisterGatingFunction registerPlugins register_plugins
show method for boolMethodshow,boolMethod-method
show method for fcFiltershow,fcFilter-method
show method for gatingTemplateshow,gatingTemplate-method
show method for gtMethodshow,gtMethod-method