openCyto: Hierarchical Gating Pipeline for flow cytometry data

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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
Date of publication
None
Maintainer
Mike Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
1.12.1

View on Bioconductor

Man pages

add
bypass the default flowWorkspace:::.addGate
add_pop
apply a gating method to the 'GatingSet'
as.data.table.gatingTemplate
convert a gatingTemplate object to a data.table
boolMethod-class
A class to represent a boolean gating method.
dims-gtMethod-method
get gating method dimensions
dummyMethod-class
A class to represent a dummy gating method that does nothing...
fcEllipsoidGate
constuctor for 'fcEllipsoidGate'
fcEllipsoidGate-class
a concrete class that reprents the ellipsoidGate generated by...
fcFilter-class
a virtual class that represents the gating result generated...
fcFilterList
constuctor for 'fcFilterList'
fcFilterList-class
a class that extends 'filterList' class.
fcPolygonGate
constuctor for 'fcPolygonGate'
fcPolygonGate-class
a concrete class that reprents the polygonGate generated by...
fcRectangleGate
constuctor for 'fcRectangleGate'
fcRectangleGate-class
a concrete class that reprents the rectangleGate generated by...
fcTree
constructor of 'fcTree'
fcTree-class
A class to represent a flowClust tree.
filterObject-logicalFilterResult-method
construct logicalGate obj
flowClust1d
Applies flowClust to 1 feature to determine a cutpoint...
flowClust2d
Automatic identification of a population of interest via...
gating-gtMethod-GatingSet-method
apply a gtMethod to the 'GatingSet'
gating-methods
Apply the gates to a GatingSet
gatingTemplate-class
a class storing the gating method and population information...
getChildren-gatingTemplate-character-method
get children nodes
getGate-fcTree-character-method
get gates saved in 'fcTree'
getGate-gatingTemplate-character-method
get gating method from the node
getNodes
get nodes from gatingTemplate object
getNodes-fcTree-method
get nodes from 'fcTree'
getParent-gatingTemplate-character-method
get parent nodes
groupBy-gtMethod-method
get the grouping variable for the gating method
gtMethod-class
A class to represent a gating method.
gtPopulation-class
A class to represent a cell population that will be generated...
gtSubsets-class
A class representing a group of cell populations.
isCollapse-gtMethod-method
get the flag that determines whether gating method is applied...
isPolyfunctional
A function to tell wether a gating method is 'polyFunctions'
listgtMethods
Print a list of the registered gating methods
mindensity
Determines a cutpoint as the minimum point of a kernel...
mindensity2
An improved version of mindensity used to determines a...
names-gtMethod-method
get gating method name
names-gtPopulation-method
get population name
ocRectangleGate-class
the class that carries event indices as well
ocRectRefGate
constructor for ocRectRefGate
ocRectRefGate-class
special gate type that mix the rectangleGate with boolean...
openCyto
Hierarchical Gating Pipeline for flow cytometry data
parameters-gtMethod-method
get parameters of the gating method/function
plot-fcFilterList-ANY-method
plot a 'fcFilterList'
plot-fcTree-character-method
plot the flowClust gating results
plot-gatingTemplate-missing-method
plot the gating scheme
polyFunctions-class
A class to represent a polyFunctions gating method.
posteriors-fcFilter-ANY-method
get posteriors from a 'fcFilter' object
ppMethod-class
A class to represent a preprocessing method.
ppMethod-gatingTemplate-character-method
get preprocessing method from the node
preprocessing-ppMethod-GatingSet-method
apply a ppMethod to the 'GatingSet'
prior_flowClust
Elicits data-driven priors from a flowSet object for...
prior_flowClust1d
Elicits data-driven priors from a flowSet object for a...
prior_kmeans
Elicits data-driven priors from a flowSet object for...
priors-fcFilter-ANY-method
get priors from a 'fcFilter' object
quadGate.seq
sequential quadrant gating function
quadGate.tmix
quadGate based on flowClust::tmixFiler
quantileGate
Determine the cutpoint by the events quantile.
refGate-class
A class to represent a reference gating method.
registerPlugins
Register a gating or preprocessing function with OpenCyto
show-boolMethod-method
show method for boolMethod
show-fcFilter-method
show method for fcFilter
show-gatingTemplate-method
show method for gatingTemplate
show-gtMethod-method
show method for gtMethod
tailgate
Gates the tail of a density using the derivative of a kernel...
templateGen
generate a partially complete csv template from the existing...
toggle.helperGates
toggle the hidden flag of the helper gates

Files in this package

openCyto/DESCRIPTION
openCyto/NAMESPACE
openCyto/R
openCyto/R/AllClasses.R
openCyto/R/RcppExports.R
openCyto/R/add.R
openCyto/R/add_pop.R
openCyto/R/as.data.table.R
openCyto/R/bayes-flowClust.R
openCyto/R/coerce.R
openCyto/R/csvTemplate-parser.R
openCyto/R/fcFilter-methods.R
openCyto/R/fcFilterList-methods.R
openCyto/R/fcTree-methods.R
openCyto/R/functions.R
openCyto/R/gating-functions.R
openCyto/R/gating-methods.R
openCyto/R/gatingTemplate-methods.R
openCyto/R/gtMethod-methods.R
openCyto/R/gtPopulation-methods.R
openCyto/R/mindensity2.R
openCyto/R/pluginFramework.R
openCyto/R/preprocessing-method.R
openCyto/R/toggle.helperGates.R
openCyto/R/unlockNamespace.R
openCyto/R/wrapper-functions.R
openCyto/R/zzz.R
openCyto/README.md
openCyto/build
openCyto/build/vignette.rds
openCyto/example
openCyto/inst
openCyto/inst/CITATION
openCyto/inst/NEWS
openCyto/inst/doc
openCyto/inst/doc/HowToAutoGating.R
openCyto/inst/doc/HowToAutoGating.Rmd
openCyto/inst/doc/HowToAutoGating.html
openCyto/inst/doc/HowToWriteCSVTemplate.R
openCyto/inst/doc/HowToWriteCSVTemplate.Rmd
openCyto/inst/doc/HowToWriteCSVTemplate.html
openCyto/inst/doc/openCytoVignette.R
openCyto/inst/doc/openCytoVignette.Rmd
openCyto/inst/doc/openCytoVignette.html
openCyto/inst/extdata
openCyto/inst/extdata/gating_template
openCyto/inst/extdata/gating_template/ICS.csv
openCyto/inst/extdata/gating_template/ICS_080.csv
openCyto/inst/extdata/gating_template/ITN_Newell.csv
openCyto/inst/extdata/gating_template/bcell.csv
openCyto/inst/extdata/gating_template/tcell.csv
openCyto/inst/extdata/gating_template/treg.csv
openCyto/inst/tests
openCyto/man
openCyto/man/add.Rd
openCyto/man/add_pop.Rd
openCyto/man/as.data.table.gatingTemplate.Rd
openCyto/man/boolMethod-class.Rd
openCyto/man/dims-gtMethod-method.Rd
openCyto/man/dummyMethod-class.Rd
openCyto/man/fcEllipsoidGate-class.Rd
openCyto/man/fcEllipsoidGate.Rd
openCyto/man/fcFilter-class.Rd
openCyto/man/fcFilterList-class.Rd
openCyto/man/fcFilterList.Rd
openCyto/man/fcPolygonGate-class.Rd
openCyto/man/fcPolygonGate.Rd
openCyto/man/fcRectangleGate-class.Rd
openCyto/man/fcRectangleGate.Rd
openCyto/man/fcTree-class.Rd
openCyto/man/fcTree.Rd
openCyto/man/filterObject-logicalFilterResult-method.Rd
openCyto/man/flowClust1d.Rd
openCyto/man/flowClust2d.Rd
openCyto/man/gating-gtMethod-GatingSet-method.Rd
openCyto/man/gating-methods.Rd
openCyto/man/gatingTemplate-class.Rd
openCyto/man/getChildren-gatingTemplate-character-method.Rd
openCyto/man/getGate-fcTree-character-method.Rd
openCyto/man/getGate-gatingTemplate-character-method.Rd
openCyto/man/getNodes-fcTree-method.Rd
openCyto/man/getNodes.Rd
openCyto/man/getParent-gatingTemplate-character-method.Rd
openCyto/man/groupBy-gtMethod-method.Rd
openCyto/man/gtMethod-class.Rd
openCyto/man/gtPopulation-class.Rd
openCyto/man/gtSubsets-class.Rd
openCyto/man/isCollapse-gtMethod-method.Rd
openCyto/man/isPolyfunctional.Rd
openCyto/man/listgtMethods.Rd
openCyto/man/mindensity.Rd
openCyto/man/mindensity2.Rd
openCyto/man/names-gtMethod-method.Rd
openCyto/man/names-gtPopulation-method.Rd
openCyto/man/ocRectRefGate-class.Rd
openCyto/man/ocRectRefGate.Rd
openCyto/man/ocRectangleGate-class.Rd
openCyto/man/openCyto.Rd
openCyto/man/parameters-gtMethod-method.Rd
openCyto/man/plot-fcFilterList-ANY-method.Rd
openCyto/man/plot-fcTree-character-method.Rd
openCyto/man/plot-gatingTemplate-missing-method.Rd
openCyto/man/polyFunctions-class.Rd
openCyto/man/posteriors-fcFilter-ANY-method.Rd
openCyto/man/ppMethod-class.Rd
openCyto/man/ppMethod-gatingTemplate-character-method.Rd
openCyto/man/preprocessing-ppMethod-GatingSet-method.Rd
openCyto/man/prior_flowClust.Rd
openCyto/man/prior_flowClust1d.Rd
openCyto/man/prior_kmeans.Rd
openCyto/man/priors-fcFilter-ANY-method.Rd
openCyto/man/quadGate.seq.Rd
openCyto/man/quadGate.tmix.Rd
openCyto/man/quantileGate.Rd
openCyto/man/refGate-class.Rd
openCyto/man/registerPlugins.Rd
openCyto/man/show-boolMethod-method.Rd
openCyto/man/show-fcFilter-method.Rd
openCyto/man/show-gatingTemplate-method.Rd
openCyto/man/show-gtMethod-method.Rd
openCyto/man/tailgate.Rd
openCyto/man/templateGen.Rd
openCyto/man/toggle.helperGates.Rd
openCyto/src
openCyto/src/RcppExports.cpp
openCyto/src/misc.cpp
openCyto/src/unlockNamespace.c
openCyto/tests
openCyto/tests/testthat
openCyto/tests/testthat.R
openCyto/tests/testthat/expectResults.rds
openCyto/tests/testthat/gating-testSuite.R
openCyto/tests/testthat/gatingResults.rds
openCyto/tests/testthat/helper-expectRes.R
openCyto/tests/testthat/test-misc.R
openCyto/tests/testthat/test-pluginFramework.R
openCyto/tests/testthat/test-template-parsing.R
openCyto/tests/testthat/test_gating_functions.R
openCyto/vignettes
openCyto/vignettes/HowToAutoGating.Rmd
openCyto/vignettes/HowToAutoGating_files
openCyto/vignettes/HowToAutoGating_files/figure-html
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-10-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-11-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-12-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-13-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-3-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-3-2.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-4-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-4-2.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-5-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-5-2.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-6-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-7-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-7-2.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-8-1.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-8-2.png
openCyto/vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-9-1.png
openCyto/vignettes/HowToWriteCSVTemplate.Rmd
openCyto/vignettes/openCytoVignette.Rmd