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Fig. 2 | Genome Biology

Fig. 2

From: EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Fig. 2

Application of EmptyDrops and other cell detection methods to one sample of the placenta dataset. a A barcode rank plot showing the fitted spline used for knee point detection in EmptyDrops. The detected knee and inflection points are also shown. b The negative log-likelihood for each barcode in the multinomial model of EmptyDrops, plotted against the total count. Barcodes detected as putative cell-containing droplets at an FDR of 0.1% are labelled in red. Only barcodes with tb>T are shown. c An UpSet plot [20] of the barcodes detected by each combination of methods (vertical bars). Horizontal bars represent the number of barcodes detected by each method. d Histogram outlines of the log-total count for barcodes detected by each method

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