Fig. 3

Dataset-level pairwise comparison of workflow performance. a The heatmap shows the relative performance of a pair of workflows, corresponding to a row and a column, directly compared to each other for the GTEx datasets based on the tissue-naive gold standard. The workflows along the rows are depicted using color swatches similar to Fig. 2. The color in each cell (row, column) represents the proportion of datasets for which the workflow along the row has a higher log2(auPRC/prior) than the workflow along the column. Comparisons that are statistically significant (corrected p < 0.01) based on a paired Wilcoxon test are marked with an asterisk. Figure S3 contains the corresponding heatmap for the SRA datasets. b, c Barplots show the number of times each workflow was significantly greater than another workflow for GTEx and SRA datasets. Figures S4 and S5 contain these performance plots based on the tissue-aware gold standard. d The table shows the most significant workflows across evaluation cases along with the number of times a given workflow outperformed any other workflow for the GTEx and SRA datasets based on the tissue-naive and tissue-aware gold standards