| attachCellScores | Attach CSOA scores to object |
| attachCellScores.default | Attach CSOA scores to object |
| attachCellScores.dgCMatrix | Attach CSOA scores to object |
| attachCellScores.matrix | Attach CSOA scores to object |
| attachCellScores.Seurat | Attach CSOA scores to object |
| attachCellScores.SingleCellExperiment | Attach CSOA scores to object |
| basicHeatmap | Plot a simple heatmap |
| breakWeakTies | Remove overlap pairs with low Jaccard scores |
| cellDistribution | Show the distribution of cell sets among cells |
| cellSetsOverlaps | Calculates the significance of overlaps of pairs of cells sets |
| connectedComponents | Find the connected components of the graph determined by the overlaps |
| expMat | Extracts the data expression matrix from object |
| expMat.default | Extracts the data expression matrix from object |
| expMat.dgCMatrix | Extracts the data expression matrix from object |
| expMat.matrix | Extracts the data expression matrix from object |
| expMat.Seurat | Extracts the data expression matrix from object |
| expMat.SingleCellExperiment | Extracts the data expression matrix from object |
| featureWes | A feature plot with a more distinctive color scheme. |
| geneRadialPlot | Radial plot for an overlap data frame |
| generateOverlaps | Generate overlaps of cell sets for input genes |
| getPairs | Get all unordered pairs of two elements from a vector |
| networkPlot | Plot the overlaps as a network |
| overlapCutoffPlot | Plot the selection of overlaps |
| overlapGenes | Get all genes from an overlap data frame |
| overlapPairs | Extract gene pairs from overlap data frame |
| percentileSets | Generates cell expressing input genes at an input percentile |
| processOverlaps | Process data frame of overlaps of cell sets |
| qGrab | Read and delete a .qs file |
| runCSOA | Run the CSOA pipeline |
| scoreCells | Generate CSOA scores from overlap data frame and list of pairs |
| scoreModules | Run CSOA separately on the connected components of the overlap graph |