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 bulkrna-ppi-networkgit 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/bulkrna-ppi-network)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/bulkrna-ppi-network"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-ppi-network/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/bulkrna-ppi-network"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-ppi-network.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 | $0.00063 | $0.01003 |
| Opus 5 | $0.00032 | $0.00502 |
| Sonnet 5 | $0.00013 | $0.00201 |
| Haiku 4.5 | $0.00006 | $0.00100 |
Grade A, and why
bulkrna-ppi-network 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 9d 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 — 85 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bulkrna-ppi-network
When to use
Run after bulkrna-de to ask "what does the STRING PPI subgraph
induced by my DEG list look like, and which proteins are central?".
Queries the public STRING API (no installation needed), constructs the
induced subgraph, and ranks hub proteins by degree centrality.
Inputs & Outputs
Inputs
- File types:
.csv,.txt
Outputs
tables/hub_genes.csvtables/interaction_edges.csvtables/node_centrality.csvfigures/hub_genes_barplot.pngfigures/ppi_network.pngreport.mdresult.json
Flow
- Parse gene list from
--input(treats first column as gene names). - Query STRING API with
species+score_threshold. - On API failure, fall back silently to built-in demo edges (
bulkrna_ppi_network.py:118warns "STRING API failed (...) — using built-in demo edges"). - Build NetworkX graph; compute degree centrality.
- Report top-N hubs; render network + degree-distribution figures.
Gotchas
- STRING-API-failure fallback is to DEMO edges, not a smaller real query.
bulkrna_ppi_network.py:118catches any API exception and substitutes the built-in toy network. This means a transient network outage produces output that looks normal but is unrelated to the user's gene list. The summary dict does not record which edge source ran — grep the run's stderr for "STRING API failed" to detect a silent fallback before reporting downstream conclusions. --score-thresholdis on STRING's 0–1000 scale, not 0–1. Default400is STRING's "medium" confidence band;700is "high";900is "highest". Passing0.4(a float) is silently coerced to0and pulls every edge in the database.--speciesis the NCBI taxon ID (default9606human,10090mouse). Passing the string"human"or"mouse"raises a type error fromint(args.species). STRING also requires the species to be in its supported list — exotic taxa fail at the API layer.- Gene-name namespace must match STRING's expectations. STRING uses HGNC symbols for human, MGI symbols for mouse. Feeding Ensembl IDs gives ~zero hits and a near-empty network — pre-run
bulkrna-geneid-mappingto convert.
What ships with it
5 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.
- 9d ago First seen · 85 lines · 63 tokens per session scan A 56b33df33779
bulkrna-ppi-network is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 63 tokens to every session and 1,003 once invoked, about $0.0003 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 2026-08-30.
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