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 skills add TianGzlab/OmicsClaw --skill spatial-integrategit 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-integrate)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-integrate"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-integrate/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-integrate"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-integrate.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Rogue Agent · line 3 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
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 5.1 | $0.00050 | $0.01198 |
| Opus 5.5 | $0.00020 | $0.00479 |
| Sonnet 5.5 | $0.00010 | $0.00240 |
| Haiku 4.5 | $0.00005 | $0.00120 |
Grade A, and why
spatial-integrate 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 14d ago.
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 — 119 lines — stays where its author put it; the contents beside it link to each section on GitHub.
spatial-integrate
Use from a step
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("spatial-integrate")
adata = read_input("data/multi_sample.h5ad")
adata = library.integrate(adata, batch_key="sample")
write_output(adata, "intermediate/integrated.h5ad")
When to use
Correct expression-space batch effects after spatial-preprocess. Harmony and Scanorama add corrected PCA-based embeddings; BBKNN replaces the neighbor graph. None aligns tissue coordinates or changes the expression matrix.
Inputs & Outputs
Input: preprocessed AnnData with obsm["X_pca"] and at least two labels in
obs["batch"] (or the chosen batch_key). Functions return AnnData, tables and
figures without writing files; see API below.
CLI writes processed.h5ad, report.md, result.json, batch-size and
integration tables, and the comparison gallery. The complete file inventory
and generation conditions are in references/output_contract.md.
Harmony adds X_pca_harmony; Scanorama adds X_scanorama;
BBKNN changes obsp["distances"] and obsp["connectivities"].
Key CLI
python skills/spatial/spatial-integrate/spatial_integrate.py \
--input multi_sample.h5ad --output results/integration --method harmony --batch-key sample
python skills/spatial/spatial-integrate/spatial_integrate.py --demo --output /tmp/spatial_integrate
Use examples/example_step.py for load_skill, saved objects and replay.
references/parameters.md lists the CLI method flags.
Gotchas
X_pcamust exist before integration; no normalization is performed here.X_scanoramais a corrected PCA-based embedding, not corrected gene expression.batch_entropy_aftermeasures local mixing, not biological preservation; inspect condition and cell-type structure before choosing a correction.- The function's seed controls Harmony, neighbors, UMAP and Leiden. BBKNN's default Annoy matching and Scanorama's wrapper expose no seed here; cross-version matching can vary. The installed versions passed repeat CLI checks.
run_info(adata, keep=False)removes only library diagnostics. The CLI keeps its existinguns["spatial_integration"]summary.X_umap_before_integrationandX_umap_after_integrationpreserve both views.
What ships with it
10 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.
- _api.py 4.7 KB runs code
- examples/example_step.py 1014 B runs code
- r_visualization/integration_publication_template.R 1.4 KB
- r_visualization/README.md 1.4 KB
- references/methodology.md 8.5 KB
- references/output_contract.md 1.7 KB
- references/parameters.md 2.4 KB
- spatial_integrate.py 38 KB runs code
- tests/test_api.py 1.3 KB runs code
- tests/test_spatial_integrate.py 15 KB runs code
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.
- 14d ago Changed · -19 lines · -12 tokens per session 27c6dc4b425c
- 1mo ago First seen · 138 lines · 62 tokens per session scan A 178c01bb5412
spatial-integrate is a skill published in the GitHub repository TianGzlab/OmicsClaw (161 stars, last pushed 14d ago), licensed Apache-2.0. It adds 50 tokens to every session and 1,198 once invoked, about $0.0002 per session on Opus 5.5. 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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