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Fig. 6 | Genome Biology

Fig. 6

From: VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies

Fig. 6

Overlap of top differentially expressed genes identified by SCDE between two data splits of the raw data or imputed data by different methods. SCDE is applied to detect genes that are differentially expressed between pairs of cell subpopulations in the Cell Type data for all pairs of seven cell types. In each comparison, cells from the two cell types are split randomly into two subsets. Imputation and differential expression analysis methods are applied to each data subset separately. The mean Jaccard index between the top 100, 200, 500, or 1000 differentially expressed genes from two subsets are computed across 10 random data splits for each imputation method as a quantification of imputation accuracy, where the Jaccard index is computed as the ratio of the intersection and the union between the top gene lists from the two subsets. Methods for comparison include DrImpute (blue), MAGIC (green), SAVER (pink), scImpute (purple), VIPER with elastic net selection (peach), and VIPER with lasso selection (dark blue)

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