Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/tiangzlab/omicsclaw/spatial-velocitynpx skills add TianGzlab/OmicsClaw --skill spatial-velocitygit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-velocity)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-velocity"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-velocity.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00091 | $0.02152 |
| Opus 5 | $0.00046 | $0.01076 |
| Sonnet 5 | $0.00018 | $0.00430 |
| Haiku 4.5 | $0.00009 | $0.00215 |
Grade A, and why
spatial-velocity scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 152 lines — stays where its author put it; the contents beside it link to each section on GitHub.
spatial-velocity
When to use
The user has a spatial AnnData with layers["spliced"] and
layers["unspliced"] populated upstream (velocyto / kb-python /
STARsolo) and wants RNA velocity estimated, with PAGA + cluster
summaries and stream / phase / spatial plots. Four backends:
stochastic(default scVelo) — moment-based, fast.deterministic(scVelo) — least-squares fit, no stochastic correction.dynamical(scVelo) — full latent-time inference viarecover_dynamics. Slow on > 5K cells; use--dynamical-n-jobs.velovi— deep generative model with latent time. Tunables--velovi-n-hidden,--velovi-n-latent,--velovi-n-layers.
Cluster column defaults to leiden (--cluster-key). For
trajectory inference without spliced layers use spatial-trajectory.
Inputs & Outputs
Inputs
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present) - Expects
obsm:spatial
Outputs
tables/cell_velocity_metrics.csvtables/gene_velocity_summary.csvtables/top_velocity_cells.csvtables/top_velocity_genes.csvtables/velocity_cell_metrics.csvtables/velocity_cluster_summary.csvtables/velocity_gene_hits.csvtables/velocity_gene_summary.csvtables/velocity_run_summary.csvtables/velocity_spatial_points.csvtables/velocity_summary.csvtables/velocity_top_cells.csvtables/velocity_top_genes.csvtables/velocity_umap_points.csvfigures/velocity_cluster_summary.pngfigures/velocity_confidence_distribution.pngfigures/velocity_confidence_spatial.pngfigures/velocity_confidence_umap.pngfigures/velocity_heatmap.pngfigures/velocity_latent_time_spatial.pngfigures/velocity_layer_proportions.pngfigures/velocity_paga.pngfigures/velocity_phase.pngfigures/velocity_pseudotime_spatial.pngfigures/velocity_speed_distribution.pngfigures/velocity_speed_spatial.pngfigures/velocity_speed_umap.pngfigures/velocity_stream_spatial.pngfigures/velocity_stream_umap.pngfigures/velocity_top_genes_barplot.pngfigures/velocity_transition_confidence_umap.pngprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:velocity_speed;var:velocity_genes;layers:velocity - When
--methodisvelovi:- AnnData additionally guarantees
obs:latent_time;var:fit_scaling;layers:latent_time_velovi,fit_t - Produces artifact
spatial.latent_timeasprocessed.h5ad(h5ad)
- AnnData additionally guarantees
What ships with it
8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- yesterday First seen · 152 lines · 91 tokens per session scan A 1ed4adc2dc73
spatial-velocity is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 91 tokens to every session and 2,152 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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