trajectory-inference
Installation
SKILL.md
Trajectory Inference
Overview
Order cells along differentiation or activation paths and estimate where each cell is heading. Output: pseudotime, velocity streams, terminal states and fate probabilities, and on spatial data their maps on the tissue with a check of whether the ordering follows space. Three layers, each optional on top of the previous one:
| Method | Needs | Gives |
|---|---|---|
| PAGA + DPT | Clusters, neighbour graph, a chosen root cluster | Cluster connectivity graph, pseudotime |
| scVelo | layers["spliced"] and layers["unspliced"] |
Direction of change per cell (velocity) |
| CellRank 2 | A transition kernel (velocity or pseudotime) | Terminal states, fate probabilities, driver genes |