assignCellCyclePhases   Cell cycle assignment
classifyCellsAndDoublets
                        Classify cells to species
collapseCellsByBarcode
                        Collapse cells by barcodes similarity
compareGeneExpressionLevels
                        Compare gene expression levels between two
                        single species samples
compareGeneExpressionLevels,MixedSpeciesSample-method
                        Compare gene expression levels between two
                        mixed species samples
compareSingleCellsAgainstBulk
                        Compare gene expression between single cell
                        sample and bulk
computeCorrelationSingleCellsVersusBulk
                        Compare single cell sample against bulk data
computeGenesPerCell     Compute genes per cell
computeMitochondrialPercentage
                        Computes mitochondrial percentage
computeTranscriptsPerCell
                        Compute transcripts per cell
extractDownstreamStatistics
                        Extract downstream statistics
extractReadStatistics   Extract statistics from mapped reads.
findInflectionPoint     Compute the inflection point / cell number.
geneExpressionDispersion
                        Compute the dispersion of each gene across all
                        cells.
geneExpressionMean      Compute the average expression of each gene
                        across all cells.
geneExpressionSumUMI    Compute the sum of transcript counts of each
                        gene across all cells.
keepBestCells           Keep best cells according to a criterion
listCellsToCollapse     List cells that are candidates for collapsing.
listCellsToCollapse,MixedSpeciesSample-method
                        List cells that are candidates for collapsing.
mergeMultipleDGEs       Merge multiple samples into a big DGE matrix
plotCellTypes           Plot separation of species
plotCumulativeFractionOfReads
                        Plots the knee plot
plotHeatmapCorrelationMatrixDGE
                        Heatmap of the correlation matrix for pairs of
                        cells.
plotHistogram           Histogram plot of an attribute
plotMitochondrialContent
                        Plot mitochondrial content
plotViolin              Violin plot of an attribute
removeCells             Remove cells by barcode
removeLowQualityCells   Filter out low quality cells
removeLowQualityGenes   Filter out low quality genes
splitDgeByGenesAndCellsOfSpecies
                        Split DGE by genes and cells of species
splitDgeByGenesOfSpecies
                        Split DGE by genes of species
splitMixedSpeciesSampleToSingleSpecies
                        Separate the mixed species sample into two
                        single species samples
