Fig. 1

Overview of CellRouter. Step (1) Starting from single cells representing multiple cell states, including stable and in transition, a gene regulatory network was built to identify putative gene regulatory relationships. Step (2) Subpopulations were identified by a combination of learning the structure of the data and community detection algorithms. Step (3) High-resolution multi-state trajectories are identified from any subpopulation to any other, including intermediate and mature cell types. Step (4) Multi-state trajectories illustrate the divergence of single-cell transcriptomes along each trajectory progression. Identification of genes implicated in the dynamic biological process under study, such as differentiation, and identification of regulators driving or mediating cell-fate transitions at the gene and network level