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| openCyto-package | Hierarchical Gating Pipeline for flow cytometry data |
| .isPolyfunctional | A function to tell wether a gating method is 'polyFunctions' |
| .prior_flowClust1d | Elicits data-driven priors from a flowSet object for a specified channel |
| .prior_kmeans | Elicits data-driven priors from a flowSet object for specified channels using the K-Means clustering algorithm |
| alias | get gating method name |
| alias-method | get gating method name |
| boolMethod-class | A class to represent a boolean gating method. |
| cytokine | Gates the tail of a density using the derivative of a kernel density estimate after standardizing and collapsing flowFrames |
| dims | get gating method name |
| dims-method | get gating method name |
| fcFilter-class | a virtual class that represents the gating result generated by flowClust gating function |
| 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 flowClust |
| fcRectangleGate | constuctor for 'fcRectangleGate' |
| fcRectangleGate-class | a concrete class that reprents the rectangleGate generated by flowClust |
| fcTree | constructor of 'fcTree' |
| fcTree-class | A class to represent a flowClust tree. |
| flowClust.1d | Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters. |
| flowClust.2d | Automatic identification of a population of interest via flowClust based on two markers |
| gating | Applies gatingTemplate to one GatingSet. |
| gating-method | Applies gatingTemplate to one GatingSet. |
| gatingTemplate | a class storing the gating method and population information in a graphNEL object |
| gatingTemplate-class | a class storing the gating method and population information in a graphNEL object |
| gatingTemplate-method | a class storing the gating method and population information in a graphNEL object |
| getChildren | get nodes from gatingTemplate object |
| getChildren-method | get nodes from gatingTemplate object |
| getGate | get nodes from gatingTemplate object |
| getGate-method | get nodes from gatingTemplate object |
| getNodes | get nodes from gatingTemplate object |
| getNodes-method | get nodes from gatingTemplate object |
| getParent | get nodes from gatingTemplate object |
| getParent-method | get nodes from gatingTemplate object |
| groupBy | get gating method name |
| groupBy-method | get gating method name |
| gtMethod-class | A class to represent a gating method. |
| gtPopulation-class | A class to represent a cell population that will be generated by a gating method. |
| gtSubsets-class | A class representing a group of cell populations. |
| isCollapse | get gating method name |
| isCollapse-method | get gating method name |
| listgtMethods | Print a list of the registered gating methods |
| mindensity | Determines a cutpoint as the minimum point of a kernel density estimate between two peaks |
| names | get gating method name |
| names-method | get gating method name |
| openCyto | Hierarchical Gating Pipeline for flow cytometry data |
| parameters | get gating method name |
| parameters-method | get gating method name |
| plot | plot a 'fcFilterList' |
| plot-method | get nodes from gatingTemplate object |
| polyFunctions-class | A class to represent a polyFunctions gating method. |
| posteriors | get posteriors from a 'fcFilter' object |
| posteriors-method | get posteriors from a 'fcFilter' object |
| ppMethod | get nodes from gatingTemplate object |
| ppMethod-class | A class to represent a preprocessing method. |
| ppMethod-method | get nodes from gatingTemplate object |
| preprocessing | apply a ppMethod to the 'GatingSet' |
| preprocessing-method | apply a ppMethod to the 'GatingSet' |
| priors | get priors from a 'fcFilter' object |
| priors-method | get priors from a 'fcFilter' object |
| prior_flowClust | Elicits data-driven priors from a flowSet object for specified channels |
| refGate-class | A class to represent a reference gating method. |
| registerPlugins | Register a gating or preprocessing function with OpenCyto |
| show | a class storing the gating method and population information in a graphNEL object |
| show-method | a class storing the gating method and population information in a graphNEL object |
| show-method | A class to represent a gating method. |
| tailgate | Gates the tail of a density using the derivative of a kernel density estimate after standardizing and collapsing flowFrames |
| templateGen | generate a partially complete csv template from the existing gating hierarchy |