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Agent skill

Tcga Gene Expression

by InternScience in InternScience/scp

Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

MITAuto-check passedResearch & Science

Install Tcga Gene Expression

skills CLI
$ npx skills add InternScience/scp --skill tcga-gene-expression -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install InternScience/scp tcga-gene-expression --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/tcga-gene-expression .claude/skills/tcga-gene-expression && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
tcga-gene-expression
GitHub stars
169
Used in
1 other repo
Token cost
~619 tokens
SKILL.md length
34 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

  • Tasks that involve Bioinformatics
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tcga Gene Expression is an agent skill from InternScience/scp. Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

Its SKILL.md is about 620 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/tcga-gene-expression”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tcga Gene Expression loads about 619 tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 34 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~34
When it runs · the whole SKILL.md, loaded when a task matches
~619

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 34 words, ~619 tokens.

Download SKILL.mdSave it as .claude/skills/tcga-gene-expression/SKILL.md (or your agent's skills folder).
name
tcga-gene-expression
description
Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.
license
MIT license
metadata.skill-author
PJLab

TCGA Gene Expression Analysis

Usage

python
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class OrigeneClient:
    def __init__(self, server_url: str, api_key: str):
        self.server_url = server_url
        self.api_key = api_key
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(url=self.server_url, headers={"SCP-HUB-API-KEY": self.api_key})
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            return False

    async def disconnect(self):
        if self.session:
            await self.session_ctx.__aexit__(None, None, None)
        if hasattr(self, 'transport'):
            await self.transport.__aexit__(None, None, None)

    def parse_result(self, result):
        if isinstance(result, dict):
            content_list = result.get("content") or []
        else:
            content_list = getattr(result, "content", []) or []
        texts = []
        for item in content_list:
            if isinstance(item, dict):
                if item.get("type") == "text":
                    texts.append(item.get("text") or "")
            else:
                if getattr(item, "type", None) == "text":
                    texts.append(getattr(item, "text", "") or "")
        return "".join(texts)

## Initialize and use
client = OrigeneClient("https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA", "<your-api-key>")
await client.connect()

result = await client.session.call_tool("get_gene_specific_expression_in_cancer_type", arguments={"gene": "TP53"})
print(client.parse_result(result))

await client.disconnect()
Tool: get_gene_specific_expression_in_cancer_type
  • Args: gene (str) - Gene symbol (e.g., "TP53")
  • Returns: High/low expression cancers with mean expression and sample counts
Use Cases
  • Cancer genomics, biomarker discovery, tumor characterization, precision oncology

© InternScience, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/tcga-gene-expression of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Tcga Gene Expression next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Tcga Gene Expression compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tcga Gene Expression this skillInternScience/scp1691 repos~619Automated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Tcga Gene Expression

What does Tcga Gene Expression do?

Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns. Tcga Gene Expression is an agent skill from InternScience/scp. Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

When should I use Tcga Gene Expression?

Tcga Gene Expression fits situations like: tasks that involve Bioinformatics.

How do I install Tcga Gene Expression in Claude Code?

Run `npx skills add InternScience/scp --skill tcga-gene-expression -a claude-code`. Or copy the skill folder (skills/tcga-gene-expression in InternScience/scp) into .claude/skills/tcga-gene-expression in your project. Claude Code loads it when a task matches its description.

How do I install Tcga Gene Expression in Codex?

Run `npx skills add InternScience/scp --skill tcga-gene-expression -a codex`. Or copy the skill folder (skills/tcga-gene-expression in InternScience/scp) into .agents/skills/tcga-gene-expression in your project. Codex loads it when a task matches its description.

Can I use Tcga Gene Expression in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add InternScience/scp --skill tcga-gene-expression -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tcga-gene-expression, .gemini/skills/tcga-gene-expression, .github/skills/tcga-gene-expression and .opencode/skills/tcga-gene-expression in your project.

What does Tcga Gene Expression need to run?

SKILL.md names no scripts, command-line tools or credentials: Tcga Gene Expression is instructions for the agent only. Our summary lists: Python 3.

Does Tcga Gene Expression access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Tcga Gene Expression safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Tcga Gene Expression use?

Tcga Gene Expression is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Tcga Gene Expression use?

About 619 tokens (SKILL.md is roughly 2.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Tcga Gene Expression?

Skills that share tags, products or a category with Tcga Gene Expression: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tcga Gene Expression?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.