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  "Title": "Hierarchical Gating Pipeline for flow cytometry data",
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  "Author": "Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo",
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    "add_pop_init",
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    "CytoExploreR_.preprocess_csv",
    "CytoExploreR_.preprocess_row",
    "delete.helperGates",
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    "flowClust.2d",
    "gate_flowclust_1d",
    "gate_flowClust_1d",
    "gate_flowclust_2d",
    "gate_flowClust_2d",
    "gate_mindensity",
    "gate_mindensity2",
    "gate_quad_sequential",
    "gate_quad_tmix",
    "gate_quantile",
    "gating",
    "gatingTemplate",
    "generate_gate_template",
    "get.helperGates",
    "getChildren",
    "getGate",
    "getNodes",
    "getParent",
    "gh_generate_template",
    "gs_add_gating_method",
    "gs_add_gating_method_init",
    "gs_remove_gating_method",
    "gt_delete_helpergates",
    "gt_gating",
    "gt_get_children",
    "gt_get_gate",
    "gt_get_helpergates",
    "gt_get_nodes",
    "gt_get_parent",
    "gt_list_methods",
    "gt_toggle_helpergates",
    "listgtMethods",
    "mindensity",
    "mindensity2",
    "plot",
    "prior_flowclust",
    "prior_flowClust",
    "quadGate.seq",
    "quadGate.tmix",
    "quantileGate",
    "register_plugins",
    "registerPlugins",
    "remove_pop",
    "show",
    "templateGen",
    "toggle.helperGates"
  ],
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      "page": "as.data.table",
      "title": "convert a gatingTemplate object to a data.table",
      "topics": [
        "as.data.table",
        "as.data.table.gatingTemplate"
      ]
    },
    {
      "page": "boolMethod-class",
      "title": "A class to represent a boolean gating method.",
      "topics": [
        "boolMethod-class"
      ]
    },
    {
      "page": "dims-gtMethod-method",
      "title": "get gating method dimensions",
      "topics": [
        "dims,gtMethod-method"
      ]
    },
    {
      "page": "dummyMethod-class",
      "title": "A class to represent a dummy gating method that does nothing but serves as reference to be refered by other population",
      "topics": [
        "dummyMethod-class"
      ]
    },
    {
      "page": "fast_rlm",
      "title": "robust linear model using an M estimator",
      "topics": [
        "fast_rlm"
      ]
    },
    {
      "page": "fcEllipsoidGate",
      "title": "constuctor for 'fcEllipsoidGate'",
      "topics": [
        "fcEllipsoidGate"
      ]
    },
    {
      "page": "fcEllipsoidGate-class",
      "title": "a concrete class that reprents the ellipsoidGate generated by flowClust",
      "topics": [
        "fcEllipsoidGate-class"
      ]
    },
    {
      "page": "fcFilter-class",
      "title": "a virtual class that represents the gating result generated by flowClust gating function",
      "topics": [
        "fcFilter-class"
      ]
    },
    {
      "page": "fcFilterList",
      "title": "constuctor for 'fcFilterList'",
      "topics": [
        "fcFilterList"
      ]
    },
    {
      "page": "fcFilterList-class",
      "title": "a class that extends 'filterList' class.",
      "topics": [
        "fcFilterList-class"
      ]
    },
    {
      "page": "fcPolygonGate",
      "title": "constuctor for 'fcPolygonGate'",
      "topics": [
        "fcPolygonGate"
      ]
    },
    {
      "page": "fcPolygonGate-class",
      "title": "a concrete class that reprents the polygonGate generated by flowClust",
      "topics": [
        "fcPolygonGate-class"
      ]
    },
    {
      "page": "fcRectangleGate",
      "title": "constuctor for 'fcRectangleGate'",
      "topics": [
        "fcRectangleGate"
      ]
    },
    {
      "page": "fcRectangleGate-class",
      "title": "a concrete class that reprents the rectangleGate generated by flowClust",
      "topics": [
        "fcRectangleGate-class"
      ]
    },
    {
      "page": "fcTree",
      "title": "constructor of 'fcTree'",
      "topics": [
        "fcTree"
      ]
    },
    {
      "page": "fcTree-class",
      "title": "A class to represent a flowClust tree.",
      "topics": [
        "fcTree-class"
      ]
    },
    {
      "page": "gate_flowclust_1d",
      "title": "Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.",
      "topics": [
        "flowClust.1d",
        "gate_flowClust_1d",
        "gate_flowclust_1d"
      ]
    },
    {
      "page": "gate_flowclust_2d",
      "title": "Automatic identification of a population of interest via flowClust based on two markers",
      "topics": [
        "flowClust.2d",
        "gate_flowClust_2d",
        "gate_flowclust_2d"
      ]
    },
    {
      "page": "gate_mindensity",
      "title": "Determines a cutpoint as the minimum point of a kernel density estimate between two peaks",
      "topics": [
        "gate_mindensity",
        "mindensity"
      ]
    },
    {
      "page": "gate_mindensity2",
      "title": "An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks.",
      "topics": [
        "gate_mindensity2",
        "mindensity2"
      ]
    },
    {
      "page": "gate_quad_sequential",
      "title": "sequential quadrant gating function",
      "topics": [
        "gate_quad_sequential",
        "quadGate.seq"
      ]
    },
    {
      "page": "gate_quad_tmix",
      "title": "quadGate based on flowClust::tmixFiler",
      "topics": [
        "gate_quad_tmix",
        "quadGate.tmix"
      ]
    },
    {
      "page": "gate_quantile",
      "title": "Determine the cutpoint by the events quantile.",
      "topics": [
        "gate_quantile",
        "quantileGate"
      ]
    },
    {
      "page": "gate_singlet",
      "title": "Creates a singlet polygon gate using the prediction bands from a robust linear model",
      "topics": [
        "gate_singlet"
      ]
    },
    {
      "page": "gatingTemplate-class",
      "title": "a class storing the gating method and population information in a graphNEL object",
      "topics": [
        "gatingTemplate",
        "gatingTemplate,character-method",
        "gatingTemplate,data.table-method",
        "gatingTemplate-class"
      ]
    },
    {
      "page": "generate_gate_template",
      "title": "Store gates from a GatingSet in a gatingTemplate for templated gating",
      "topics": [
        "generate_gate_template"
      ]
    },
    {
      "page": "getGate-fcTree-character-method",
      "title": "get gates saved in 'fcTree'",
      "topics": [
        "getGate,fcTree,character-method"
      ]
    },
    {
      "page": "getNodes-fcTree-method",
      "title": "get nodes from 'fcTree'",
      "topics": [
        "getNodes,fcTree-method"
      ]
    },
    {
      "page": "gh_generate_template",
      "title": "generate a partially complete csv template from the existing gating hierarchy",
      "topics": [
        "gh_generate_template",
        "templateGen"
      ]
    },
    {
      "page": "groupBy-gtMethod-method",
      "title": "get the grouping variable for the gating method",
      "topics": [
        "groupBy,gtMethod-method"
      ]
    },
    {
      "page": "gs_add_gating_method",
      "title": "apply a gating method to the 'GatingSet'",
      "topics": [
        "add_pop",
        "gs_add_gating_method"
      ]
    },
    {
      "page": "gs_add_gating_method_init",
      "title": "Clear history of 'gs_add_gating_method' calls for a given 'GatingSet' or 'GatingSetList'",
      "topics": [
        "add_pop_init",
        "gs_add_gating_method_init"
      ]
    },
    {
      "page": "gs_remove_gating_method",
      "title": "Reverse the action of gating methods applied via 'gs_add_gating_method'",
      "topics": [
        "gs_remove_gating_method",
        "remove_pop"
      ]
    },
    {
      "page": "gt_gating",
      "title": "Applies a gatingTemplate to a GatingSet.",
      "topics": [
        "gating",
        "gating,gatingTemplate,GatingSet-method",
        "gt_gating",
        "gt_gating,gatingTemplate,GatingSet-method",
        "gt_gating.gatingTemplate"
      ]
    },
    {
      "page": "gt_get_children",
      "title": "get children nodes",
      "topics": [
        "getChildren",
        "getChildren,gatingTemplate,character-method",
        "gt_get_children"
      ]
    },
    {
      "page": "gt_get_gate",
      "title": "get gating method from the node",
      "topics": [
        "getGate,gatingTemplate,character-method",
        "gt_get_gate"
      ]
    },
    {
      "page": "gt_get_nodes",
      "title": "get nodes from gatingTemplate object",
      "topics": [
        "getNodes",
        "getNodes,gatingTemplate-method",
        "gt_get_nodes"
      ]
    },
    {
      "page": "gt_get_parent",
      "title": "get parent nodes",
      "topics": [
        "getParent",
        "getParent,gatingTemplate,character-method",
        "gt_get_parent"
      ]
    },
    {
      "page": "gt_list_methods",
      "title": "Print a list of the registered gating methods",
      "topics": [
        "gt_list_methods",
        "listgtMethods"
      ]
    },
    {
      "page": "gt_toggle_helpergates",
      "title": "toggle/delete the hidden flag of the helper gates",
      "topics": [
        "delete.helperGates",
        "get.helperGates",
        "gt_delete_helpergates",
        "gt_get_helpergates",
        "gt_toggle_helpergates",
        "toggle.helperGates"
      ]
    },
    {
      "page": "gtMethod-class",
      "title": "A class to represent a gating method.",
      "topics": [
        "gtMethod",
        "gtMethod-class"
      ]
    },
    {
      "page": "gtPopulation-class",
      "title": "A class to represent a cell population that will be generated by a gating method.",
      "topics": [
        "gtPopulation-class"
      ]
    },
    {
      "page": "gtSubsets-class",
      "title": "A class representing a group of cell populations.",
      "topics": [
        "gtSubsets-class"
      ]
    },
    {
      "page": "isCollapse-gtMethod-method",
      "title": "get the flag that determines whether gating method is applied on collapsed data",
      "topics": [
        "isCollapse,gtMethod-method"
      ]
    },
    {
      "page": "names-gtMethod-method",
      "title": "get gating method name",
      "topics": [
        "names,gtMethod-method"
      ]
    },
    {
      "page": "names-gtPopulation-method",
      "title": "get population name",
      "topics": [
        "names,gtPopulation-method"
      ]
    },
    {
      "page": "ocRectangleGate-class",
      "title": "the class that carries event indices as well",
      "topics": [
        "ocRectangleGate-class"
      ]
    },
    {
      "page": "ocRectRefGate",
      "title": "constructor for ocRectRefGate",
      "topics": [
        "ocRectRefGate"
      ]
    },
    {
      "page": "ocRectRefGate-class",
      "title": "special gate type that mix the rectangleGate with boolean gate",
      "topics": [
        "ocRectRefGate-class"
      ]
    },
    {
      "page": "openCyto",
      "title": "Hierarchical Gating Pipeline for flow cytometry data",
      "topics": [
        "openCyto-package",
        "openCyto"
      ]
    },
    {
      "page": "openCyto-deprecated",
      "title": "Deprecated functions in package 'openCyto'.",
      "topics": [
        "openCyto-deprecated"
      ]
    },
    {
      "page": "openCyto.options",
      "title": "Some global options for openCyto See examples for the meaning of these options and how to get/set them.",
      "topics": [
        "openCyto.options"
      ]
    },
    {
      "page": "parameters-gtMethod-method",
      "title": "get parameters of the gating method/function",
      "topics": [
        "parameters,gtMethod-method"
      ]
    },
    {
      "page": "plot-fcFilterList-ANY-method",
      "title": "plot a 'fcFilterList'",
      "topics": [
        "plot,fcFilterList,ANY-method"
      ]
    },
    {
      "page": "plot-fcTree-character-method",
      "title": "plot the flowClust gating results",
      "topics": [
        "plot,fcTree,character-method"
      ]
    },
    {
      "page": "plot-gatingTemplate-missing-method",
      "title": "plot the gating scheme",
      "topics": [
        "plot,gatingTemplate,ANY-method",
        "plot,gatingTemplate,character-method",
        "plot,gatingTemplate,missing-method",
        "plot,gatingTemplate-method"
      ]
    },
    {
      "page": "polyFunctions-class",
      "title": "A class to represent a polyFunctions gating method.",
      "topics": [
        "polyFunctions-class"
      ]
    },
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      "page": "add",
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