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m.jiang
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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@86108 bc3139a8-67e5-0310-9ffc-ced21a209358
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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$

‎.gitignore

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src/*.o
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src/*.so
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.Rproj.user
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*.Rproj
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.Rhistory

‎DESCRIPTION

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Package: openCyto
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Type: Package
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Title: Hierarchical Gating Pipeline for flow cytometry data
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Version: 1.1.9
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Date: 2012-06-10
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Author: Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo
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Maintainer: Mike Jiang <[email protected]>
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Description: This package is designed to facilitate the automated gating
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methods in sequential way to mimic the manual gating strategy.
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License: Artistic-2.0
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LazyLoad: yes
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Collate:
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'AllGenerics.R'
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'AllClasses.R'
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'bayes-flowClust.R'
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'functions.R'
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'gating-methods.R'
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'gating-functions.R'
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'gatingTemplate-methods.R'
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'gtMethod-methods.R'
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'gtPopulation-methods.R'
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'fcFilterList-methods.R'
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'fcTree-methods.R'
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'fcFilter-methods.R'
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'wrapper-functions.R'
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'preprocessing-method.R'
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'pluginFramework.R'
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'unlockNamespace.R'
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Depends:
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methods,flowWorkspace (>= 3.9.47)
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Imports:
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Biobase,gtools,flowCore,flowStats,flowClust,MASS,clue,plyr,RBGL,Rgraphviz,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
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Suggests:
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flowWorkspaceData (>= 1.99.12),
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knitr
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biocViews: FlowCytometry, DataImport, Preprocessing, DataRepresentation
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#Enhances: flowDensity
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VignetteBuilder: knitr

‎NAMESPACE

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export(.between_interval)
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export(cytokine)
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export(flowClust.1d)
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export(flowClust.2d)
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export(listgtMethods)
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export(mindensity)
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export(prior_flowClust)
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export(registerGatingFunction)
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export(tailgate)
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export(templateGen)
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exportClasses(gatingTemplate)
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exportClasses(gtMethod)
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exportClasses(gtPopulation)
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exportClasses(ppMethod)
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exportMethods(alias)
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exportMethods(dims)
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exportMethods(gating)
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exportMethods(gatingTemplate)
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exportMethods(getChildren)
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exportMethods(getGate)
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exportMethods(getNodes)
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exportMethods(getParent)
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exportMethods(groupBy)
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exportMethods(isCollapse)
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exportMethods(names)
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exportMethods(parameters)
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exportMethods(plot)
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exportMethods(ppMethod)
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exportMethods(show)
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import(flowWorkspace)
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import(utils)
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importClassesFrom(Biobase,AssayData)
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importClassesFrom(flowCore,filterList)
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importClassesFrom(flowCore,polygonGate)
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importClassesFrom(flowCore,rectangleGate)
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importClassesFrom(graph,graph)
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importClassesFrom(graph,graphBase)
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importClassesFrom(graph,graphNEL)
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importClassesFrom(rrcov,Ulist)
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importClassesFrom(rrcov,Uvector)
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importFrom(Biobase,dims)
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importFrom(clue,solve_LSAP)
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importFrom(data.table,fread)
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importFrom(flowClust,dmvt)
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importFrom(flowClust,dmvtmix)
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importFrom(flowClust,filter)
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importFrom(flowClust,getEstimates)
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importFrom(flowClust,rbox)
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importFrom(flowClust,tmixFilter)
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importFrom(flowStats,quadrantGate)
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importFrom(flowStats,rangeGate)
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importFrom(flowStats,singletGate)
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importFrom(flowStats,warpSet)
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importFrom(graph,"edgeData<-")
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importFrom(graph,"edgeDataDefaults<-")
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importFrom(graph,"nodeData<-")
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importFrom(graph,"nodeDataDefaults<-")
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importFrom(graph,addEdge)
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importFrom(graph,edgeData)
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importFrom(graph,edgeDataDefaults)
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importFrom(graph,edges)
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importFrom(graph,graphNEL)
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importFrom(graph,inEdges)
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importFrom(graph,nodeData)
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importFrom(graph,nodeDataDefaults)
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importFrom(graph,subGraph)
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importFrom(gtools,permutations)
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importFrom(ks,drvkde)
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importFrom(ks,hpi)
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importFrom(MASS,huber)
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importFrom(plyr,aaply)
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importFrom(plyr,laply)
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importFrom(plyr,ldply)
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importFrom(R.utils,isPackageInstalled)
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importFrom(RBGL,tsort)
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importFrom(RColorBrewer,brewer.pal)
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useDynLib(openCyto)

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