assignCellCyclePhases | Cell cycle assignment |
classifyCellsAndDoublets | Classify cells to species |
collapseCellsByBarcode | Collapse cells by barcodes similarity |
compareGeneExpressionLevels | Compare gene expression levels between two single species... |
compareGeneExpressionLevels-MixedSpeciesSample-method | Compare gene expression levels between two mixed species... |
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... |
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... |
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