...

In Partek Flow, we use tools from Monocle 3 [1] to build trajectories, identify states and branch points, and calculate pseudotime values. The output of Trajectory analysis task includes an interactive 2D/3D visualization for viewing the trajectory trees and setting the root states (starting points of the trajectories). From the Trajectory analysis report, you can run a second task, Calculate pseudotime, which adds a numeric cell-level attribute, Pseudotime, calculated using the chosen root states. 

Major updates in Monocle 3 (compared to Monocle 2) include:

• Monocle 3 learns the principal trajectory graph in the UMAP space;
• the principal graph is smoothened and small branches are excluded;
• support for principal graphs with loops and convergences.

Setting up Trajectory Analysis

...