Man pages for rajewsky-lab/dropseq

assignCellCyclePhasesCell cycle assignment
classifyCellsAndDoubletsClassify cells to species
collapseCellsByBarcodeCollapse cells by barcodes similarity
compareGeneExpressionLevelsCompare gene expression levels between two single species...
compareGeneExpressionLevels-MixedSpeciesSample-methodCompare gene expression levels between two mixed species...
compareSingleCellsAgainstBulkCompare gene expression between single cell sample and bulk
computeCorrelationSingleCellsVersusBulkCompare single cell sample against bulk data
computeGenesPerCellCompute genes per cell
computeMitochondrialPercentageComputes mitochondrial percentage
computeTranscriptsPerCellCompute transcripts per cell
extractDownstreamStatisticsExtract downstream statistics
extractReadStatisticsExtract statistics from mapped reads.
findInflectionPointCompute the inflection point / cell number.
geneExpressionDispersionCompute the dispersion of each gene across all cells.
geneExpressionMeanCompute the average expression of each gene across all cells.
geneExpressionSumUMICompute the sum of transcript counts of each gene across all...
keepBestCellsKeep best cells according to a criterion
listCellsToCollapseList cells that are candidates for collapsing.
listCellsToCollapse-MixedSpeciesSample-methodList cells that are candidates for collapsing.
mergeMultipleDGEsMerge multiple samples into a big DGE matrix
plotCellTypesPlot separation of species
plotCumulativeFractionOfReadsPlots the knee plot
plotHeatmapCorrelationMatrixDGEHeatmap of the correlation matrix for pairs of cells.
plotHistogramHistogram plot of an attribute
plotMitochondrialContentPlot mitochondrial content
plotViolinViolin plot of an attribute
removeCellsRemove cells by barcode
removeLowQualityCellsFilter out low quality cells
removeLowQualityGenesFilter out low quality genes
splitDgeByGenesAndCellsOfSpeciesSplit DGE by genes and cells of species
splitDgeByGenesOfSpeciesSplit DGE by genes of species
splitMixedSpeciesSampleToSingleSpeciesSeparate the mixed species sample into two single species...
rajewsky-lab/dropseq documentation built on Feb. 23, 2018, 11:13 a.m.