Man pages for tchitchek-lab/SPADEVizR
SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results
| abundantClustersViewer | Visualization of abundant clusters |
| AC-class | Abundant Clusters (AC) class definition |
| annotateClusters | Annotating cell clusters |
| AP-class | Abundance Profiles (AP) class definition |
| assignContext-methods | Assignement of a context into a 'Results' object |
| biplotViewer | Visualization of marker co-expression |
| boxplotViewer | Visualization of cluster enrichment profiles conditions |
| CC-class | Correlated Clusters (CC) class definition |
| circlesPackingViewer | Visualization of abundance profiles classification |
| classifyAbundanceProfiles | Classification of clustering results based on the abundance... |
| correlatedClustersViewer | Visualization of correlated clusters |
| countViewer | Visualization of cluster sizes |
| createReport | Generating SPADEVizR reports |
| DAC-class | Differentially Abundant Clusters (DAC) class definition |
| distogramViewer | Visualization of marker co-expressions |
| export-methods | Exportation of SPADEVizR objects |
| generateCPHM | Generation of a Cox proportional hazards regression model of... |
| generateGLM | Generation a generalized linear models of cluster abundances |
| generateRFM | Generation of a random forest of cluster abundances |
| heatmapViewer | Visualization of all clusters phenotypes using categorical... |
| identifyAC | Identification of the Abundant Clusters |
| identifyCC | Identification of the correlation of SPADE cluster with a... |
| identifyDAC | Identification of the Differentially Abundant Clusters |
| importResultsFromCLR.ACS | Importation of clustering results from a folder containing... |
| importResultsFromCLR.CSV | Importation of clustering results from a folder containing... |
| importResultsFromFCS | Importation of clustering results from a folder containing... |
| importResultsFromSPADE | Importation of clustering results generated by SPADE |
| importResultsFromTables | Importation of clustering results from text files |
| kineticsViewer | Visualization of cluster enrichment profiles kinetics |
| load.flowSet | Loading of FCS files object into a 'Results' object |
| MDSViewer | Visualization of SPADE cluster or sample similarities using... |
| mergeClusters | Merging of cell clusters from a Results object |
| phenoViewer | Visualization of cluster phenotypes |
| plot-methods | Visualization for all SPADEVizR objects |
| print-methods | Textual previews for all SPADEVizR objects |
| qcSmallClusters | Computing of the fraction of clusters with low number of... |
| qcUniformClusters | Computing of the fraction of cluster with uniform phenotypes |
| removeClusters | Removing of cell clusters from a Results object |
| Results-class | Results class definition |
| show-methods | Textual previews for SPADEVizR objects |
| streamgraphViewer | Visualization of cluster abundance dynamics |
| treeViewer | Visualization of combined SPADE trees |
| unload.flowSet-methods | Unload 'flowSet' object from a 'Results' object |
| volcanoViewer | Visualization of differentially abundant clusters |
