spade: SPADE -- An analysis and visualization tool for Flow Cytometry

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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 <bjornson@stanford.edu>
License
GPL-2
Version
1.20.0
URLs

View on Bioconductor

Man 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.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

Files in this package

spade/DESCRIPTION
spade/LICENSE
spade/NAMESPACE
spade/R
spade/R/annotation.R
spade/R/autoAssign.R
spade/R/cluster.R
spade/R/downsample.R
spade/R/driver.R
spade/R/fcs.R
spade/R/upsample.R
spade/R/zzz.R
spade/README.md
spade/build
spade/build/vignette.rds
spade/cleanup
spade/configure
spade/configure.ac
spade/inst
spade/inst/doc
spade/inst/doc/SPADE.R
spade/inst/doc/SPADE.Rnw
spade/inst/doc/SPADE.pdf
spade/inst/extdata
spade/inst/extdata/SimulatedRawData.fcs
spade/inst/tools
spade/inst/tools/CytoSPADE.jar
spade/inst/tools/organize_fold_pdfs.sh
spade/inst/tools/organize_median_pdfs.sh
spade/inst/tools/runSPADE.R
spade/m4
spade/m4/ac_openmp.m4
spade/man
spade/man/SPADE.FCSToTree.Rd
spade/man/SPADE.addClusterToFCS.Rd
spade/man/SPADE.addDensityToFCS.Rd
spade/man/SPADE.annotateGraph.Rd
spade/man/SPADE.downsampleFCS.Rd
spade/man/SPADE.driver.Rd
spade/man/SPADE.flattenAnnotations.Rd
spade/man/SPADE.installPlugin.Rd
spade/man/SPADE.layout.arch.Rd
spade/man/SPADE.markerMedians.Rd
spade/man/SPADE.plot.trees.Rd
spade/man/SPADE.read.FCS.Rd
spade/man/SPADE.write.graph.Rd
spade/src
spade/src/Makevars
spade/src/Makevars.in
spade/src/Makevars.win
spade/src/cluster.cc
spade/src/downsample.cc
spade/src/spade.cc
spade/src/upsample.cc
spade/src/util.h
spade/vignettes
spade/vignettes/SPADE.Rnw
spade/vignettes/cytospade.png
spade/vignettes/science-tree-cd34.png
spade/vignettes/spaderef.bib