SPADE is a visualization and analysis tool for high-dimensional flow cytometry data. SPADE is implemented as an R package and can be installed via R's packaging facilities. Additionally a GUI is provided, as a Cytoscape plugin, for setting-up and interactively visualizing the results of SPADE analyses. Please see the project homepage at cytospade.org or the wiki for the primary documentation.
Please refer to the wiki pages, especially the Getting Started page.
- R 3.x. Note that many of SPADE's dependencies are no longer available for R 2.15.x as of October 2013.
- igraph
- flowCore
The SPADE package has a C++ core that must be built before use. SPADE successfully builds on Linux, OSX and Windows (with Rtools), although Windows users will not be able to take advantage of the OpenMP parallelization used within SPADE. SPADE can be installed from the command line via
$ R CMD INSTALL <SPADE PATH>
On Windows, you will need to install the Rtools that matches your R distribution. After installation make sure that your PATH contains the neccessary Rtools binary directories, e.g.:
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Open Control Panel -> System
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Click on Advanced Tab and then on Environment Variables
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Highlight PATH and click Edit
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In the character string in Variable Value, make sure the following appear (before other/older compilers):
c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\Program Files\R<your R version>\bin;
Source packages can be built with
$ R CMD build <SPADE PATH>
and binary packages with
$ R CMD build --no-vignettes --binary <SPADE PATH>
SPADE was developed in the Plevritis and Nolan Labs at Stanford University, and is described in the following publications:
- Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP, "CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data". Bioinformatics, 2012.
- Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs, Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, "Phenotypically determined self-organization of flow cytometry data with spanning-tree progression analysis of density normalized events". Nature Biotechnolgy, 2011.
- Sean C. Bendall, Erin F. Simonds, Peng Qiu, El-ad D. Amir, Peter O. Krutzik, Rachel Finck, Robert V. Bruggner, Rachel Melamed, Angelica Trejo, Olga I. Ornatsky, Robert S. Balderas, Sylvia K. Plevritis, Karen Sachs, Dana Pe’er, Scott D. Tanner, Garry P. Nolan, "Single-Cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum", Science, 332 (6030): 687-696.
- Michael D. Linderman, Erin F. Simonds, Peng Qiu, Zach Bjornson, Nikesh Kotecha, Teresa H. Meng, Sylvia Plrevritis, Garry P. Nolan, "Algorithmically recovering the hematopoietic lineage from high-dimensional cytometry data using SPADE", Congress of the Intl. Society for Advancement of Cytometry, 2010.