Computational Molecular Biology 2025, Vol.15, No.2, 91-101 http://bioscipublisher.com/index.php/cmb 95 Figure 1 Identification and developmental trajectories of early cell types (Adopted from Finkbeiner et al., 2022) 5 Inference of 5 Pathways and Cell Fate Trajectories One of the key goals of single-cell data analysis is to reconstruct the trajectory of cell differentiation, that is, to infer the sequence of their development or transformation processes based on the continuity of molecular characteristics between cells. Trajectory inference, also known as pseudotime analysis, has many mature methods in scRNA-seq data (such as Monocle, Slingshot, PAGA, etc.) (Durmaz and Scott, 2022). These methods are usually based on measuring the distances between cells in a high-dimensional expression space, and then looking for curves or trees in a low-dimensional space to represent the gradual relationship of cell states. Through
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