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Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. First, Luca Pinello will set the stage presenting the basic concepts of how to build a trajectory inference approach from scratch (a cookbook perspective). Then Huidong Chen will describe the method behind STREAM - a novel Elastic Principal Graph implementation (ElPiGraph), followed by a detailed discussion of how to visualize the learned trajectory and how to discover branch-specific genes, or genes differentiating between trajectory branches. We will close off with examining what we have learned so far and what the future directions and challenges are.