Man pages for JinmiaoChenLab/cytofkit2
cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets
| ClusterX | Fast clustering by automatic search and find of density peaks |
| 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... |
| cytof_exprsMerge | Merge the expression matrix from multiple FCS files with... |
| cytof_heatmap | Heatmap plot of cluster mean value results |
| cytofkit | cytofkit2: an integrated mass cytometry data analysis... |
| cytofkit2-package | cytofkit2: an integrated mass cytometry data analysis... |
| cytofkitNews | check the package update news |
| cytofkitShinyAPP | A Shiny APP to interactively visualize the analysis results |
| cytofkit_shiny_dashboard | Title |
| 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 |
| Rphenograph | RphenoGraph clustering |
| spectral1 | First Function for spectral color palette |
| spectral2 | Second Function for spectral color palette |
