Spanning tree
Progression of
Density normalized

The SPADE algorithm was originally developed by Peng Qiu in Sylvia Plevritis' lab in collaboration with Garry P. Nolan's laboratory to visualize and analyze high-dimensional flow cytometry data, and especially data collected with the CyToF mass cytometer. SPADE and its use is described in the following publications/abstracts:

SPADE was implemented in Garry P. Nolan's Laboratory by Michael Linderman, Erin Simonds, Zach Bjornson, Robert Bruggner and Ketaki Sheode. The SPADE Cytoscape plugin includes code generously supplied by Cytobank under the AGPL license. SPADE is in wide use within the Nolan Laboratory as stand-alone tool and as part of the Cytobank online single-cell analysis platform.

Tools for visualizing and analyzing high-dimensional flow cytometry data is an important and vibrant area of research. The above publication has a rich related work section that situates SPADE in the context of other advances tools in this field, including probability state modeling with Gemstone, SAMSpectral (Zare, et al., BMC Bioinformatics, 2010.) and many others.

© 2011 Garry P. Nolan Laboratory, Stanford University

Work partially supported by: NIH RO1CA130826-01 and other sources