dropbead

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Documentation for package ‘dropbead’ version 0.3.1

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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-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-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