|SPADE.addClusterToFCS||Annotate observations in FCS file with cluster assignment|
|SPADE.addDensityToFCS||Annotate FCS file with local density of each observation|
|SPADE.annotateGraph||Add attributes to graph|
|SPADE.downsampleFCS||Downsample observcations in a FCS file according to density...|
|SPADE.driver||SPADE workflow driver|
|SPADE.FCSToTree||Cluster and build minimum spanning tree from data in FCS...|
|SPADE.flattenAnnotations||Flatten list of annotations to matrix|
|SPADE.installPlugin||Install CytoSPADE Cytoscape plugin|
|SPADE.layout.arch||Generate coordinates for plotting graphs|
|SPADE.markerMedians||Compute marker medians, coefficient of variations and counts...|
|SPADE.plot.trees||Plot trees with annotated vertices|
|SPADE.read.FCS||Read an FCS File|
|SPADE.write.graph||Writing the graph to a file in some format|
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