# dropbead

## Documentation for package ‘dropbead’ version 0.3.1

- DESCRIPTION file.

## Help Pages

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