Table 1.
Overview of different trajectory inference algorithms.
| Method | Description | Software |
|---|---|---|
| Monocle 2 (45) | Multiple branching, optional number of end states | Monocle [R] |
| Diffusion Pseudotime (46) | Single branching event (Destiny), multiple branching (Scanpy) | Destiny (47) [R], Scanpy (48) [Python] |
| Slingshot (49) | Multiple branching, optional start and end clusters | Slingshot [R] |
| GPfates (50) | Multiple branching, optional time course as pseudotime prior, computationally demanding (use for <1,000 cells only) | GPfates [Python] |
| TSCAN (51) | Multiple branching | TSCAN [R] |
| AGA (52) | Graph | Scanpy (48) [Python] |
| Wishbone (53) | Single branching event | Wishbone [Python] |