Regulatory network-based imputation of dropouts in single-cell RNA sequencing data
Fig 4
Detection of cell type-specific markers before and after imputation.
A) Number of significant (FDR < 0.05, |log2FC| > 0.25) cell type markers detected with no dropout imputation and using the tested imputation methods. Horizontal dashed lines correspond to the number of markers detected irrespectively of imputation. The fraction of the bar in a darker shade corresponds to the number of markers detected exclusively when using a given imputation approach. B) and C) fraction of captured high confidence terms, defined as significantly enriched (p.value < 0.001 and log2Enrichment > 0.5, Methods) GO biological process terms among the cluster markers detected without imputation. B) Sensitivity: fraction of high confidence terms detected as significantly enriched (p.value < 0.001 and log2Enrichment > 0.5) among the cluster markers detected with each imputation method. C) log2-enrichment of all high confidence terms among the cluster markers detected with each imputation method. DEC: definitive endoderm cells; EC: endothelial cells; H9: undifferentiated human embryonic stem cells; HFF: human foreskin fibroblasts; NPC: neural progenitor cells; TB: trophoblast-like cells.