Table 5 Overview of accuracy and performance running scSplit on five multiplexed scRNA-seq datasets, with one CPU and 30 GB RAM
From: Genotype-free demultiplexing of pooled single-cell RNA-seq
scSplit vs demuxlet | Mix 1 | Mix 2 | Mix 3 | Mix 4 | Mix 5 |
|---|---|---|---|---|---|
Mixed samples | 7 | 8 | 8 | 8 | 7 |
Number of cells | 914 | 8 137 | 5 165 | 6 977 | 7 428 |
Reads per cell | 86 148 | 16 386 | 21 265 | 18 572 | 19 657 |
informative SNVs | 15 848 | 26 830 | 26 162 | 23 224 | 41 993 |
Build matrices | 10 min | 23 min | 18 min | 21 min | 35 min |
Assign cells | 4 min | 47 min | 23 min | 45 min | 50 min |
Singlet TPR | 0.94 | 0.93 | 0.94 | 0.93 | 0.93 |
Singlet FDR | 0.06 | 0.07 | 0.06 | 0.07 | 0.07 |
Doublet TPR | 0.52 | 0.17 | 0.15 | 0.17 | 0.08 |
Doublet FDR | 0.48 | 0.83 | 0.85 | 0.83 | 0.92 |
Cohen’s Kappa | 0.86 | 0.78 | 0.68 | 0.77 | 0.76 |