Monocle 3 has been re-engineered to analyze large, complex single-cell datasets.
The algorithms at the core of Monocle 3 are highly scalable and can handle millions of cells.
Monocle 3 adds some powerful new features that enable the analysis of organism- or embryo-scale experiments:
A better structured workflow to learn developmental trajectories.
Support for the UMAP algorithm to initialize trajectory inference.
Support for trajectories with multiple roots.
Ways to learn trajectories that have loops or points of convergence.