CytoML.par.init         workspace version is parsed from xml node
                        '/Workspace/version' in flowJo workspace and
                        matched with this list to dispatch to the one
                        of the three workspace parsers
CytoML.par.set          CytoML.par.set sets a set of parameters in the
                        CytoML package namespace.
GatingSet,character,character-method
                        constructors for GatingSet
GatingSet2cytobank      Convert a GatingSet to a Cytobank-compatible
                        gatingML
GatingSet2flowJo        Convert a GatingSet to flowJo workspace
addCustomInfo           add customInfo nodes to each gate node and add
                        BooleanAndGates
compensate,GatingSet,graphGML-method
                        compensate a GatingSet based on the
                        compensation information stored in graphGML
                        object
constructTree           Reconstruct the population tree from the
                        GateSets
cytobankExperiment      Construct cytobank_experiment object from ACS
                        file
cytobank_to_gatingset.default
                        A wrapper that parse the gatingML and FCS files
                        (or cytobank_experiment object) into GatingSet
diva_workspace-class    diva_workspace class Inherited from
                        flowjo_workspace-class
extend                  extend the gate to the minimum and maximum
                        limit of both dimensions based on the bounding
                        information.
flowjo_workspace-class
                        An R representation of a flowJo workspace.
gating,graphGML,GatingSet-method
                        Apply the gatingML graph to a GatingSet
getChildren,graphGML,character-method
                        get children nodes
getCompensationMatrices.graphGML
                        Extract compensation from graphGML object.
getFJWSubsetIndices     Fetch the indices for a subset of samples in a
                        flowJo workspace, based on a keyword value pair
getGate,graphGML,character-method
                        get gate from the node
getKeywords             Get Keywords
getNodes,graphGML-method
                        get nodes from graphGML object
getParent,graphGML,character-method
                        get parent nodes
getSampleGroups         Get a table of sample groups from a flowJo
                        workspace
getSamples              Get a list of samples from a flowJo workspace
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
openDiva                open Diva xml workspace
open_flowjo_xml         Open/Close a flowJo workspace
parse.gateInfo          Parse the cytobank custom_info for each gate
parseWorkspace,flowjo_workspace-method
                        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
