Package: openCyto 2.19.0

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

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openCyto.pdf |openCyto.html✨
openCyto/json (API)
NEWS

# Install 'openCyto' in R:
install.packages('openCyto', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:openCyto-2.17.1(bioc 3.20)openCyto-2.16.1(bioc 3.19)

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

immunooncologyflowcytometrydataimportpreprocessingdatarepresentation

7.54 score 1 packages 350 scripts 1.1k downloads 11 mentions 51 exports 69 dependencies

Last updated 23 days agofrom:d3a4d87bdf. Checks:OK: 1 WARNING: 3 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64ERROROct 30 2024
R-4.5-linux-x86_64WARNINGOct 30 2024
R-4.4-win-x86_64ERROROct 30 2024
R-4.4-mac-x86_64ERROROct 30 2024
R-4.4-mac-aarch64WARNINGOct 15 2024
R-4.3-win-x86_64ERROROct 30 2024
R-4.3-mac-aarch64ERROROct 30 2024
R-4.3-mac-x86_64WARNINGOct 15 2024

Exports:add_popadd_pop_initCytoExploreR_.argDeparserCytoExploreR_.preprocess_csvdelete.helperGatesflowClust.1dflowClust.2dgate_flowclust_1dgate_flowClust_1dgate_flowclust_2dgate_flowClust_2dgate_mindensitygate_mindensity2gate_quad_sequentialgate_quad_tmixgate_quantilegatinggatingTemplateget.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:abindBHBiobaseBiocGenericsclicolorspacecpp11crayoncytolibdata.tableDelayedArraydeldirdplyrfansifarverflowClustflowCoreflowVizflowWorkspacegenericsggplot2gluegraphgtablehexbinIDPmiscinterpIRangesisobandjpegKernSmoothlabelinglatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellncdfFlownlmepillarpkgconfigpngR6RBGLRColorBrewerRcppRcppEigenRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsscalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVectorzlibbioc

An Introduction to the openCyto package

Rendered fromopenCytoVignette.Rmdusingknitron Oct 30 2024.

Last update: 2022-10-24
Started: 2014-02-05

OpenCyto: How to use different auto gating functions

Mike Jiang

Rendered fromHowToAutoGating.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-10-24
Started: 2016-06-02

How to write a csv gating template

Rendered fromHowToWriteCSVTemplate.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-11-09
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
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
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
rewrite huber estimatorrobust_m_estimator
show method for boolMethodshow,boolMethod-method
show method for fcFiltershow,fcFilter-method
show method for gatingTemplateshow,gatingTemplate-method
show method for gtMethodshow,gtMethod-method