# cytofkit: an integrated mass cytometry data analysis pipeline

## Documentation for package ‘cytofkit’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cytofkit-package | cytofkit: an integrated mass cytometry data analysis pipeline
ClusterX | Fast clustering by automatic search and find of density peaks
cytofkit | cytofkit: an integrated mass cytometry data analysis pipeline
cytofkitNews | check the package update news
cytofkitShinyAPP | A Shiny APP to interactively visualize the analysis results
cytofkit_GUI | Function for launching the user friendly GUI client for 'cytofkit-package'
cytof_addToFCS | Add data to the original FCS files
cytof_cluster | Subset detection by clustering
cytof_clusterMtrx | Expression values by cluster
cytof_clusterPlot | Scatter plot of the cluster results
cytof_clusterStat | Statistics of the cluster results
cytof_colorPlot | Plot the data with color-coded marker values
cytof_dimReduction | Dimension reduction for high dimension data
cytof_exprsExtract | Extract the expression data from a FCS file with preprocessing
cytof_exprsMerge | Merge the expression matrix from multiple FCS files with preprocessing
cytof_heatmap | Heatmap plot of cluster mean value results
cytof_progression | Progression estimation of cytof expression data
cytof_progressionPlot | Progression plot
cytof_writeResults | Save the cytofkit analysis results
DensVM | Density-based local maxima cluster with SVM
fixedLogicleParameters_GUI | GUI for gettting parameter for logicle transformation
getParameters_GUI | GUI for marker selection
launchShinyAPP_GUI | GUI for launching shiny APP
Rphenograph | RphenoGraph clustering
spectral1 | First Function for spectral color palette
spectral2 | Second Function for spectral color palette