dropkick outperforms analogous methods on challenging data sets. (A) UMAP embedding of all barcodes kept by dropkick_label (dropkick score ≥ 0.5), CellRanger_2, and EmptyDrops for human colorectal carcinoma inDrop samples. Points colored by each of the three filtering labels, as well as clusters determined by NMF analysis, dropkick score (cell probability), arcsinh-transformed total genes detected, percentage counts mitochondrial, and original batch. 3907_S1 is normal human colonic mucosa, and 3907_S2 is colorectal carcinoma from the same patient. (B) Dot plot showing top differentially expressed genes for each NMF cluster. The size of each dot indicates the percentage of cells in the population with nonzero expression for the given gene, and the color indicates the average expression value in that population. Bracketed genes indicate significantly enriched or depleted populations in dropkick compared with CellRanger_2 and/or EmptyDrops labels as shown in C. (C) Table and bar graph enumerating the total number of barcodes detected by each algorithm in all NMF clusters for the combined data set. Significant cluster enrichment as determined by sc-UniFrac is denoted by brackets.
