Step 5 : Reporting

The final step in the scMRD pipeline constructs per-patient HTML reports that visualize the somatic alterations, clonal architecture, protein signatures, and quality control (QC) plots for the sample. The summary page visualizes the clonal architecture, somatic mutation zygosity per clone, protein expression per clone, and two tables providing detailed information and annotation for each clone and mutation. Additional advanced data visualizations are included, such as a phylogenetic tree, protein UMAP, protein co-expression plot, and QC plots for demultiplexing.