Appendix A Model details

The red lines in the bottom plot indicate linear fits and the red axis labels show the rank correlation coefficients ρ and p values. The matrix is orthogonal, thus avoiding a singular design. As scGen returns corrected input data, we performed PCA on the output data, which were used for further evaluation (cf. Appendix Section A.1). Here, we used the same number of principle components (PCs) as used for Embedded cells are colored by dataset. In Figure 9, we present the results of the simulation experiments discussed in the main text.