# SPADE -- An analysis and visualization tool for Flow Cytometry

## Documentation for package ‘spade’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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