├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── CytoNorm.R ├── QuantileNorm.R ├── evaluation.R ├── helperFunctions.R ├── plotDensities.R ├── plotRidgelines.R └── plotSplines.R ├── README.md ├── inst └── extdata │ ├── Gates_PTLG021_Unstim_Control_1.fcs │ ├── Gates_PTLG021_Unstim_Control_2.fcs │ ├── Gates_PTLG028_Unstim_Control_1.fcs │ ├── Gates_PTLG028_Unstim_Control_2.fcs │ ├── Gates_PTLG034_Unstim_Control_1.fcs │ └── Gates_PTLG034_Unstim_Control_2.fcs ├── man ├── CytoNorm.normalize.Rd ├── CytoNorm.train.Rd ├── PlotOverviewCV.Rd ├── QuantileNorm.normalize.Rd ├── QuantileNorm.train.Rd ├── cytofTransform.Rd ├── cytofTransform.reverse.Rd ├── emdEvaluation.Rd ├── figures │ └── algorithm_overview.PNG ├── getCytoNormQuantiles.Rd ├── getDensities.Rd ├── getQuantiles.Rd ├── identityFunction.Rd ├── madEvaluation.Rd ├── named.list.Rd ├── plotDensities.Rd ├── plotRidgelines.Rd ├── plotSplines.Rd ├── prepareFlowSOM.Rd ├── testCV.Rd └── textPlot.Rd └── vignettes ├── .gitignore ├── CytoNorm_channels_without_clustering.Rmd ├── CytoNorm_channels_without_clustering.md ├── CytoNorm_channels_without_clustering_files └── figure-gfm │ ├── EMD and MAD figures-1.png │ ├── Evaluate densities-1.png │ ├── Evaluate splines-1.png │ └── Evaluate splines-2.png ├── CytoNorm_towards_distribution.Rmd ├── CytoNorm_towards_distribution.md ├── CytoNorm_towards_distribution_files └── figure-gfm │ ├── EMD and MAD figures-1.png │ ├── Evaluate densities-1.png │ ├── Evaluate splines-1.png │ └── Evaluate splines-2.png ├── CytoNorm_without_controls.Rmd ├── CytoNorm_without_controls.md └── CytoNorm_without_controls_files └── figure-gfm ├── EMD and MAD figures-1.png ├── Evaluate CVs-1.png ├── Evaluate CVs-2.png ├── Evaluate CVs-3.png ├── Evaluate densities-1.png ├── Evaluate splines-1.png ├── Evaluate splines-2.png ├── Evaluate splines-3.png └── Evaluate splines-4.png /.Rbuildignore: -------------------------------------------------------------------------------- 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