We used R to generate all plots (R version 4.1, 4.2 and 4.3). We generated UpSet plots using ComplexHeatmap (v.2.10.0)103. To generate the circos plots, we used circlize (v.0.4.15)104. We generated enrichment heatmaps, gene term enrichment, error plots, box plots, distribution plots and scatterplots using a combination of ggplot2 (v.3.3.6)105 and ggpubr (v.0.4.15)106. For the pairwise comparison plots, we used corrplot (v.0.92)107. We generated metaplots using the mashr function mash_plot_meta. We generated Venn diagrams with ggvenn (v.0.1.10).
