To showcase how SwitchTFI can be used to derive novel and at the same biologically meaningful hypotheses for datasets where prior knowledge on cell state transition mechanisms is scarce, we used it to reanalyze scRNA-seq data [52] of CD4-positive type 1 T helper (Th1) cells from murine liver and spleen tissues 10 days post infection with the Armstrong and Docile strains of the lymphocytic choriomeningitis virus (LCMV) that induce an acute and a chronic infection, respectively [53, 54]. Here, CD4 is linked to infection.