Fig. 2.

Method concordance and output characteristics. a A dendrogram representation of the hierarchical clustering of methods based on the proportion of shared genes in the at most top 20 genes they select. Methods are labeled by the package which implements them, whether they select only up-regulated marker genes or both up- and down-regulated marker genes, and whether they output a set of marker genes or a ranking of genes by strength of marker gene status. b A variety of features summarizing (averaging over datasets) the characteristics of the at most top 5 marker genes methods select. Methods are sorted by alphabetical order. c Three features (Area under the curve, log fold-change and Cohen’s d) summarizing (averaging over datasets) the one-vs-rest effect size of the at most top 5 marker genes that methods select. The three features are quantile normalized and methods are ranked by the median score across datasets