addCustomInfo           add customInfo nodes to each gate node and add
                        BooleanAndGates
ce_get_channels         Extract channels from cytobank_experiment
ce_get_compensations    Obtain the spillover matrices for the samples
                        in a Cytobank experiment
ce_get_markers          Extract markers from cytobank_experiment
ce_get_panels           Obtain counts of the number of samples
                        associated with each marker panel in a Cytobank
                        experiment
ce_get_samples          Obtain a mapping between the samples and marker
                        panels in a Cytobank experiment
ce_get_transformations
                        Obtain the transformations associated with each
                        channel in a Cytobank experiment
compensate,GatingSet,graphGML-method
                        compensate a GatingSet based on the
                        compensation information stored in graphGML
                        object
constructTree           Reconstruct the population tree from the
                        GateSets
cytobank_experiment-methods
                        Methods for interacting with
                        cytobank_experiment objects
cytobank_to_gatingset   A wrapper that parses the gatingML and FCS
                        files (or 'cytobank_experiment' object) into
                        GatingSet
CytoML-deprecated       Deprecated functions in package 'CytoML'.
diva_get_samples        Get a table of samples from a FACSDiva
                        workspace
diva_to_gatingset       Parse a FACSDiva Workspace
diva_workspace-class    An R representation of a BD FACSDiva workspace
extend                  extend the gate to the minimum and maximum
                        limit of both dimensions based on the bounding
                        information.
fj_ws_get_keywords      Get Keywords
fj_ws_get_sample_groups
                        Get a table of sample groups from a flowJo
                        workspace
fj_ws_get_samples       Get a list of samples from a flowJo workspace
flowjo_workspace-class
                        An R representation of a flowJo workspace.
gatingset_to_cytobank   Convert a GatingSet to a Cytobank-compatible
                        gatingML
gatingset_to_flowjo     Convert a GatingSet to flowJo workspace
getChildren,graphGML,character-method
                        get children nodes
getCompensationMatrices.graphGML
                        Extract compensation from graphGML object.
getGate,graphGML,character-method
                        get gate from the node
getNodes,graphGML-method
                        get nodes from graphGML object
getParent,graphGML,character-method
                        get parent nodes
getTransformations.graphGML
                        Extract transformations from graphGML object.
graphGML-class          A graph object returned by
                        'read.gatingML.cytobank' function.
gs_compare_cytobank_counts
                        compare the counts to cytobank's exported csv
                        so that the parsing result can be verified.
matchPath               Given the leaf node, try to find out if a
                        collection of nodes can be matched to a path in
                        a graph(tree) by the bottom-up searching
open_cytobank_experiment
                        Construct a 'cytobank_experiment' object from
                        ACS file
open_diva_xml           open Diva xml workspace
open_flowjo_xml         Open/Close a flowJo workspace
parse.gateInfo          Parse the cytobank custom_info for each gate
parseWorkspace          Parse a flowJo Workspace
plot,graphGML,missing-method
                        plot the population tree stored in graphGML.
range.GatingHierarchy   the parameter range from the flow data
                        associated with GatingHierarchy
read.gatingML.cytobank
                        Parser for gatingML exported by Cytobank
show,graphGML-method    show method for graphGML
