Fig. 2
From: Classification of low quality cells from single-cell RNA-seq data
Biology and technical features of low quality cells. a, b Comparison of the levels of gene expression and noise for Gene Ontology (GO) terms between broken (a), multiples (b), and high quality cells. The logarithm (log10) of P values from a two-sided paired t-test using mean normalized read count (x-axis) and Distance-to-Median (DM) (y-axis) was computed for each GO category and plotted against each other by multiplying the sign of the t-statistic. c Boxplots of biological and d technical features comparing log10 transformed values (y-axis) between each type of low quality (multiple, broken, empty) and high quality cells (x-axis). Each dot corresponds to one cell. GO categories labeled green indicate upregulation in high quality cells. GO categories labeled red indicate upregulation in low quality cells. e Principal component analysis of single cells from different cell types. Cells from different experiments (or laboratories) but the same cell type are presented in the same color. Using all features results in a clear distinction between each type. Removing features causing this separation results in a set of common features applicable to any cell type and protocol