# cytofkit: an integrated analysis pipeline for mass cytometry data

## Documentation for package ‘cytofkit’ version 1.1.0

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

## Help Pages

cytofkit-package | cytofkit: an integrated analysis pipeline for mass cytometry data
add_col_to_fcs | Add new columns to the fcs expression data
cluster_gridPlot | Grid scatter plot of the cluster results with multiple samples
cluster_plot | Scatter plot of the cluster results
clust_mean_heatmap | Heatmap plot of cluster mean value results
clust_percentage_heatmap | Heatmap plot of cluster percentage results
clust_state | Statistical analysis of the cluster results
cytofkit | cytofkit: an integrated analysis pipeline for mass cytometry data
cytof_dimReduction | Dimension reduction of CyTof expression data
cytof_tsne_densvm | CyTOF data analysis for subpopulation detection
cytof_tsne_densvm_GUI | The user friendly GUI for function 'cytof_tsne_densvm'
cytof_write_results | Save the cytofkit analysis results
densVM_cluster | Density-based local maxima cluster with SVM
fcs_lgcl | Transformation of the FCS data
fcs_lgcl_merge | merge the transformed expression data of FCS file(s) of selected markers
peaksGamma_plot | Plot varaition of peak nums with increasing gamma