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.annotateMarkers | Compute marker medians, coefficient of variations and counts for clusters |
SPADE.density | Annotate FCS file with local density of each observation |
SPADE.downsampleFCS | Downsample observcations in a FCS file according to density parameter |
SPADE.driver | SPADE workflow driver |
SPADE.FCSToTree | Cluster and build minimum spanning tree from data in FCS files |
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 for clusters |
SPADE.plot.trees | Plot trees with annotated vertices |
SPADE.read.FCS | Read an FCS File |
SPADE.transform.FCS | Annotate FCS file with local density of each observation |
SPADE.write.graph | Writing the graph to a file in some format |