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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
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Overview
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