SPADE, or Spanning tree Progression of Density normalized Events, is an analysis and visualization tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.
|Author||M. Linderman, P. Qiu, E. Simonds, Z. Bjornson|
|Date of publication||None|
|Maintainer||Zach Bjornson <firstname.lastname@example.org>|
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