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.
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skillsWrote 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/commands/zamushwani/biomedical-ai-skills/query-tcga)<a href="https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/query-tcga"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/query-tcga/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/commands/zamushwani/biomedical-ai-skills/query-tcga"><img src="https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/query-tcga.svg" alt="Reviewed on agentmods" width="80" 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 5.1 | $0.00037 | $0.00366 |
| Opus 5 | $0.00018 | $0.00183 |
| Sonnet 5 | $0.00007 | $0.00073 |
| Haiku 4.5 | $0.00004 | $0.00037 |
Grade A, and why
query-tcga scanned grade A with 1 finding 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 12d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read Grep Glob Bash(python3 *) Bash(curl *) What it actually says
Query the GDC for project $0, gene $1.
Follow the biomedical-mcp skill. Call the GDC REST API directly (https://api.gdc.cancer.gov) rather than wrapping TCGAbiolinks, which is R and calls the same API underneath.
The parts that are usually got wrong:
- There is no expression matrix endpoint. Querying
/filesfor expression returns tens of thousands of file references; you POST the ids to/data/{file_id}and assemble the matrix yourself. A tool promising a matrix from one call cannot deliver. - Clinical fields need
expand=demographic,diagnoses. Without it, cases come back near-empty and look like missing data. /ssmsis distinct mutations;/ssm_occurrencesis mutation-in-a-case. A cohort mutation count is almost always the occurrence count.- Paginate with
from/size, not page numbers. The response carriespagination.total. - Several fields are lists even when they look scalar —
primary_siteis['Bronchus and lung'], not a string. - Record the data release from
/status; results change between releases.
Report: the query issued, the pagination total, and the data release the answer came from.
If $0 is empty, list candidate TCGA projects first.
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.
- 12d ago First seen · 23 lines · 0 tokens per session scan A a5cd5c9b12bb
query-tcga is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 13d ago), licensed MIT. It adds 37 tokens to every session and 366 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other commands, from other repositories
read
Accepts: local PDF path, DOI, journal URL, or a pasted abstract with basic metadata.
feed
Execute all steps without asking for user confirmation at intermediate stages. Report results at the end.
critic
Deep-review a specific cluster with CellTypePilot's Annotation Critic.
ctp-inspect
Inspect single-cell data — auto-detect species, tissue, clusters, embeddings.
faostat-country-profile
Generate a food security and agricultural profile for a country.
vehicle-comparison
Side-by-side comparison of launch vehicles — cost, payload, reusability.