cbioportal-database

cbioportal-database is a skill for Claude Code from jaechang-hits/SciAgent-Skills. It costs 82 tokens per session (8,658 once invoked), scanned A, original, no licence file.

A cancer genomics data connector for cBioPortal, a service that collects genetic and clinical information from cancer studies such as TCGA. It retrieves mutations, copy-number changes, gene activity, treatment, stage, and survival data.

In plain words
What is it for?
Use it to study mutation frequencies, tumour mutation burden, gene changes across cancers, oncoprints, and links between genetic changes and survival or treatment.
Why use it?
It removes the need to find and combine these cancer-study records manually. It helps compare many studies using a consistent data source.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the sciagent-skills plugin — 146 skills shipped together

Good fit Use it to study mutation frequencies, tumour mutation burden, gene changes across cancers, oncoprints, and links between genetic changes and survival or treatment.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/cbioportal-database
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.

Any agent
npx skills add jaechang-hits/SciAgent-Skills --skill cbioportal-database
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 146 skills.

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 cbioportal-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/cbioportal-database/github.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/cbioportal-database)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/cbioportal-database"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/cbioportal-database/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 cbioportal-database

Your own site · 80×15
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/cbioportal-database"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/cbioportal-database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 82 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,658 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 unknown 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 $0.00082 $0.08658
Opus 5 $0.00041 $0.04329
Sonnet 5 $0.00016 $0.01732
Haiku 4.5 $0.00008 $0.00866

Measured 12d ago against content hash f3d9fcf5a2fa, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

cbioportal-database 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.

r = requests.get(f"{BASE_URL}/{endpoint}", params=params,
skills/genomics-bioinformatics/databases/cbioportal-database/SKILL.md · 797 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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. 12d ago First seen · 797 lines · 82 tokens per session scan A f3d9fcf5a2fa

Subscribe to this mod's changes

cbioportal-database is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (362 stars, last pushed 14d ago), with no licence file. It adds 82 tokens to every session and 8,658 once invoked, about $0.0004 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 2026-08-30.

Related

Other skills, from other repositories