Calculate per-cell gene signature scores using cell set overlaps

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Documentation for package ‘CSOA’ version 0.99.2

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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