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-communicationgit 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-communication)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-communication"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-communication/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-communication"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-communication.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 | $0.00057 | $0.01313 |
| Opus 5.5 | $0.00023 | $0.00525 |
| Sonnet 5.5 | $0.00011 | $0.00263 |
| Haiku 4.5 | $0.00006 | $0.00131 |
Grade A, and why
spatial-communication 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 17d 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 — 128 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Spatial communication
When to use
Infer ligand-receptor interactions between annotated populations. LIANA is the default; CellPhoneDB and FastCCC need a local CellPhoneDB database. CellChat runs in an R subprocess. These methods do not constrain interactions by spatial distance: coordinates support the CLI maps, not the inference.
API
Use load_skill("spatial-communication") in an analysis step.
examples/example_step.py uses real PBMC expression with explicitly synthetic
coordinates. The CLI demo uses synthetic expression and is not biological evidence.
communicate(adata, *, method='liana', cell_type_key='leiden', species='human', random_state=None, **parameters)
Infer ligand-receptor interactions and return the same AnnData.
LIANA uses raw when present, otherwise X. Other backends read normalized X. Coordinates support CLI maps; these methods do not impose distance filters.
:param adata: Log-normalized expression with cell-type labels; modified in place. :param method: CLI default liana; cellphonedb, fastccc or cellchat_r also supported. :param cell_type_key: CLI default leiden; obs column defining populations. :param species: CLI default human; mouse supported by LIANA and CellChat. :param random_state: None keeps LIANA seed 1337 and CellChat seed 1; CellPhoneDB uses 0. :param parameters: Native backend keywords in references/parameters.md. :returns: The same AnnData with canonical ccc_results and role summaries in uns. :raises ValueError: Method, labels, species or numeric controls are invalid. :raises ImportError: Optional backend is missing; use install_skill_deps. :raises FileNotFoundError: CellPhoneDB/FastCCC's local database is missing.
interactions(adata, *, significant_only=False)
Return ligand-receptor scores; unmeasured p values remain missing.
:param adata: AnnData returned by communicate. :param significant_only: Default False; True selects real p values below 0.05. :returns: A new DataFrame with ligand, receptor, source, target, score and pvalue. :raises ValueError: No run is recorded.
What ships with it
12 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 4.6 KB runs code
- examples/example_step.py 1.2 KB runs code
- r_visualization/communication_publication_template.R 1.7 KB
- r_visualization/README.md 1.6 KB
- references/methodology.md 1.9 KB
- references/output_contract.md 2.4 KB
- references/parameters.md 4.1 KB
- rscripts/cellchat.R 8.0 KB
- spatial_communication.py 44 KB runs code
- tests/test_api.py 3.6 KB runs code
- tests/test_example_replay.py 1.8 KB runs code
- tests/test_spatial_communication.py 12 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.
- 17d ago Changed · -21 lines · -25 tokens per session 0aa7bd4f2204
- 1mo ago First seen · 149 lines · 82 tokens per session scan A dfe6345bc8c6
spatial-communication is a skill published in the GitHub repository TianGzlab/OmicsClaw (161 stars, last pushed 17d ago), licensed Apache-2.0. It adds 57 tokens to every session and 1,313 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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