single-trajectory-analysis
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-trajectory --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single-trajectory analysis skill ## Overview This skill describes how to reproduce and extend the single-trajectory analysis workflow in `omicverse`, combining graph-based trajectory inference, RNA velocity coupling, and downstream fate scoring notebooks. ## Trajectory setup - **PAGA (Partition-based graph abstraction)** - Build a neighborhood graph (`pp.neighbors`) on the preprocessed AnnData object. - Use `tl.paga` to compute cluster connectivity and `tl.draw_graph` or `tl.umap` with `init_pos='paga'` for embedding. - Interpret edge weights to prioritize branch resolution and seed paths. - **Palantir** - Run `Palantir` on diffusion components, seeding with manually selected start cells (e.g., naïve T cells). - Extract pseudotime, branch probabilities, and differentiation potential for subsequent overlays. - **VIA** - Execute `via.VIA` on the kNN graph to identify lineage progression with automatic root selection or user-defined roots. - Export terminal states and pseudotime for cross-validation against PAGA and Palantir results. ## Velocity coupling (VIA + scVelo) - Use `scv.pp.filter_and_normalize`, `scv.pp.moments`, and `scv.tl.velocity` to generate velocity layers. - Provide
- Overview
- Trajectory setup
- Velocity coupling (VIA + scVelo)
- Downstream fate scoring notebooks
- Required preprocessing
- Parameter tuning
- Visualization and export
- Troubleshooting tips
What does the single-trajectory-analysis skill do?
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-trajectory --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.