CytoML: GatingML interface for openCyto

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This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

Author
Mike Jiang
Date of publication
None
Maintainer
Mike Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

addCustomInfo
add customInfo nodes to each gate node and add...
compare.counts
compare the counts to cytobank's exported csv so that the...
compensate-GatingSet-graphGML-method
compensate a GatingSet based on the compensation information...
constructTree
Reconstruct the population tree from the GateSets
cytobank2GatingSet
A wrapper that parse the gatingML and FCS files into...
extend
extend the gate to the minimum and maximum limit of both...
gating-methods
Apply the gatingML graph to a GatingSet
GatingSet2cytobank
Convert a GatingSet to a Cytobank-compatible gatingML
GatingSet2flowJo
Convert a GatingSet to flowJo workspace
getChildren-graphGML-character-method
get children nodes
getCompensationMatrices-graphGML-method
Extract compensation from graphGML object.
getGate-graphGML-character-method
get gate from the node
getNodes-graphGML-method
get nodes from graphGML object
getParent-graphGML-character-method
get parent nodes
getTransformations-graphGML-method
Extract transformations from graphGML object.
graphGML-class
A graph object returned by 'read.gatingML.cytobank' function.
matchPath
Given the leaf node, try to find out if a collection of nodes...
parse.gateInfo
Parse the cytobank custom_info for each gate
plot-graphGML-missing-method
plot the population tree stored in graphGML.
read.gatingML.cytobank
Parser for gatingML exported by Cytobank
show-graphGML-method
show method for graphGML

Files in this package

CytoML/DESCRIPTION
CytoML/NAMESPACE
CytoML/R
CytoML/R/GatingSet2cytobank.R
CytoML/R/GatingSet2flowJo.R
CytoML/R/cytobank2GatingSet.R
CytoML/R/flowUtils_functions.R
CytoML/R/graphGML_methods.R
CytoML/R/read.gatingML.cytobank.R
CytoML/R/utils.R
CytoML/README.md
CytoML/build
CytoML/build/vignette.rds
CytoML/inst
CytoML/inst/NEWS
CytoML/inst/doc
CytoML/inst/doc/HowToExportGatingSet.R
CytoML/inst/doc/HowToExportGatingSet.Rmd
CytoML/inst/doc/HowToExportGatingSet.html
CytoML/inst/doc/HowToParseGatingML.R
CytoML/inst/doc/HowToParseGatingML.Rmd
CytoML/inst/doc/HowToParseGatingML.html
CytoML/inst/extdata
CytoML/inst/extdata/cytotrol_tcell_cytobank.xml
CytoML/inst/extdata/cytotrol_tcell_cytobank_counts.csv
CytoML/inst/tests
CytoML/man
CytoML/man/GatingSet2cytobank.Rd
CytoML/man/GatingSet2flowJo.Rd
CytoML/man/addCustomInfo.Rd
CytoML/man/compare.counts.Rd
CytoML/man/compensate-GatingSet-graphGML-method.Rd
CytoML/man/constructTree.Rd
CytoML/man/cytobank2GatingSet.Rd
CytoML/man/extend.Rd
CytoML/man/gating-methods.Rd
CytoML/man/getChildren-graphGML-character-method.Rd
CytoML/man/getCompensationMatrices-graphGML-method.Rd
CytoML/man/getGate-graphGML-character-method.Rd
CytoML/man/getNodes-graphGML-method.Rd
CytoML/man/getParent-graphGML-character-method.Rd
CytoML/man/getTransformations-graphGML-method.Rd
CytoML/man/graphGML-class.Rd
CytoML/man/matchPath.Rd
CytoML/man/parse.gateInfo.Rd
CytoML/man/plot-graphGML-missing-method.Rd
CytoML/man/read.gatingML.cytobank.Rd
CytoML/man/show-graphGML-method.Rd
CytoML/tests
CytoML/tests/testthat
CytoML/tests/testthat.R
CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R
CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R
CytoML/tests/testthat/helper-lib.R
CytoML/tests/testthat/test-cytobank.R
CytoML/tests/testthat/test-extend.R
CytoML/tests/testthat/test-flowJo.R
CytoML/vignettes
CytoML/vignettes/HowToExportGatingSet.Rmd
CytoML/vignettes/HowToParseGatingML.Rmd
CytoML/vignettes/cytobank.png
CytoML/vignettes/flowJo.png