Fig. 1

Overview of the mitch workflow. The mitch package consists of five functions (left). The mitch_import function recognises the format of commonly used differential omics tools such as DESeq2, edgeR and limma and performs ranking of each contrast, to create a multi contrast rank table. If user’s would like to use a different ranking scheme, mitch_import can be bypassed in favour of a custom ranking approach. The gmt_import function reads gene matrix transposed files (GMT). The mitch_calc function determines the degree of enrichment of each gene set in the multi contrast table, yielding a mitch result object. The mitch_report function produces a single HTML format report of results containing several tables and charts. The mitch_plots function generates high resolution PDF containing charts derived from the mitch results. Example minimal mitch analysis code (right) to determine the enrichment of gene sets obtained from a GMT file in two dimensions, represented as two edgeR top tables