Man pages for rajewsky-lab/dropbead
dropbead
| 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... |
