Trajectory Analysis

Overview

Reconstructs continuous cell-state transitions from single-cell RNA-seq. Four layers:

1. Diffusion pseudotime (scanpy.tl.dpt) — orders cells along a diffusion manifold from a user-specified root.
2. PAGA — coarse-grained cluster connectivity; initializes force-directed layouts.
3. RNA velocity (scVelo) — directional flow from unspliced/spliced mRNA ratios. Note: scVelo is in maintenance mode (no new features); APIs remain stable.
4. CellRank v2 — unified kernel API combining velocity, pseudotime, real-time, or CytoTRACE signals into a Markov chain for macrostates, terminal states, and fate probabilities. CytoTRACEKernel enables velocity-free trajectory inference.

Inputs assume a preprocessed AnnData (normalized, log-transformed, HVGs, neighbors computed). Velocity additionally requires spliced/unspliced layers from velocyto or STARsolo.

Usage

Describe the analysis in natural language: