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query-tcga

query-tcga is a command for Claude Code from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (366 once invoked), scanned A, original, MIT.

A command for querying the Genomic Data Commons, a public cancer-data system, for TCGA projects, mutations, and clinical information.

In plain words
What is it for?
Use it to query a project and gene, inspect mutation occurrences, retrieve clinical variables, and report the request, result count, and data release.
Why use it?
It helps retrieve cancer cohort data while accounting for pagination, clinical fields, mutation-count definitions, and changing data releases.

Command for Claude Code

Written for Claude Code: allowed-tools in frontmatter. Also seen: positional $N argument.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to query a project and gene, inspect mutation occurrences, retrieve clinical variables, and report the request, result count, and data release.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/zamushwani/biomedical-ai-skills/query-tcga
View source ↗ zamushwani/biomedical-ai-skills
Install

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.

Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code.

Wrote 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.

agentmods badge for query-tcga

README.md
[![agentmods](https://agentmods.dev/badge/commands/zamushwani/biomedical-ai-skills/query-tcga/github.svg)](https://agentmods.dev/commands/zamushwani/biomedical-ai-skills/query-tcga)
Your own site
<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.

agentmods 80×15 button for query-tcga

Your own site · 80×15
<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>
Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 366 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.00366
Opus 5.5 $0.00000 $0.00146
Sonnet 5.5 $0.00000 $0.00073
Haiku 4.5 $0.00000 $0.00037

Measured 2mo ago against content hash a5cd5c9b12bb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 2mo 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 *)
.claude/commands/query-tcga.md · 23 lines

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:

  1. There is no expression matrix endpoint. Querying /files for 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.
  2. Clinical fields need expand=demographic,diagnoses. Without it, cases come back near-empty and look like missing data.
  3. /ssms is distinct mutations; /ssm_occurrences is mutation-in-a-case. A cohort mutation count is almost always the occurrence count.
  4. Paginate with from/size, not page numbers. The response carries pagination.total.
  5. Several fields are lists even when they look scalar — primary_site is ['Bronchus and lung'], not a string.
  6. 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.

Changes

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.

  1. 2mo ago First seen · 23 lines · 0 tokens per session scan A a5cd5c9b12bb

Subscribe to this mod's changes

query-tcga is a command published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 366 tokens. 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.

DESeq2ResearchScientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

query-tcga compared with commands from other repositories

query-tcga next to 6 commands from other repositories
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