# Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

## Documentation for package ‘CSOA’ version 1.3.1

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

## Help Pages

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
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
overlapCutoffPlot | Plot the selection of overlaps
overlapGenes | Get all genes from an overlap data frame
overlapNetworkPlot | Plot the overlaps as a network
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 .qs2 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