omicverse-single-cell-trajectory-inference

What problem does it solve?

Provide reproducible trajectory inference and coarse lineage summarization for cluster-ready single-cell AnnData objects so users can compute pseudotime, fate probabilities, and cluster-level topology without redoing preprocessing.

Core Features & Use Cases

• Multi-branch inference: Run diffusion_map, slingshot, or palantir branches through a shared TrajInfer wrapper to obtain dpt_pseudotime, slingshot_pseudotime, or palantir_pseudotime and associated outputs.
• Palantir follow-ups: Compute fate probabilities, branch masks, and optional lineage gene trends when dependencies are present.
• PAGA topology: Produce cluster-level PAGA summaries and visualizations after pseudotime computation to aid interpretation.
• Use Case: Convert an OmicVerse trajectory notebook into a reusable workflow to compare DPT, Slingshot, and Palantir analyses on the same preprocessed dataset.

Quick Start

Run diffusion_map on my cluster-ready AnnData to compute pseudotime and then calculate and plot a PAGA topology summary.