├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── ClusterX.R ├── DensVM.R ├── RcppExports.R ├── Rphenograph.R ├── cytof_cluster.R ├── cytof_dimensionReduction.R ├── cytof_postProcess.R ├── cytof_preProcess.R ├── cytof_progression.R ├── cytofkit.R ├── cytofkit_GUI.R └── cytofkit_shinyAPP.R ├── README.md ├── _config.yml ├── inst ├── CITATION ├── NEWS.Rd ├── extdata │ ├── 130515_C2_stim_CD19-.fcs │ ├── demo_fcs.RData │ ├── help.gif │ ├── help.png │ └── parameter.txt ├── shiny │ ├── global.R │ ├── server.R │ └── ui.R └── unitTests │ └── test_cytof_dimReduction.R ├── man ├── ClusterX.Rd ├── DensVM.Rd ├── Rphenograph.Rd ├── cytof_addToFCS.Rd ├── cytof_cluster.Rd ├── cytof_clusterMtrx.Rd ├── cytof_clusterPlot.Rd ├── cytof_clusterStat.Rd ├── cytof_colorPlot.Rd ├── cytof_dimReduction.Rd ├── cytof_exprsExtract.Rd ├── cytof_exprsMerge.Rd ├── cytof_heatmap.Rd ├── cytof_progression.Rd ├── cytof_progressionPlot.Rd ├── cytof_writeResults.Rd ├── cytofkit-package.Rd ├── cytofkit.Rd ├── cytofkitNews.Rd ├── cytofkitShinyAPP.Rd ├── cytofkit_GUI.Rd ├── fixedLogicleParameters_GUI.Rd ├── getParameters_GUI.Rd ├── launchShinyAPP_GUI.Rd ├── spectral1.Rd └── spectral2.Rd ├── src ├── .gitignore ├── RcppExports.cpp ├── cytofkit.dll └── jaccard_coeff.cpp ├── tests └── runTests.R └── vignettes ├── cluster_panel.png ├── cytofkit_GUI.png ├── cytofkit_example.Rmd ├── cytofkit_pipeline.png ├── cytofkit_shinyAPP.Rmd ├── cytofkit_workflow.Rmd ├── load2shiny.png ├── logo.png ├── marker_panel.png ├── progression_panel.png └── sample_panel.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinmiaoChenLab/cytofkit/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinmiaoChenLab/cytofkit/HEAD/DESCRIPTION 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