Agent skill

Region Gene Elements

Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

MITAuto-check passedResearch & Science

Install Region Gene Elements

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a claude-code

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

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements --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/region-gene-elements .claude/skills/region-gene-elements && 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/

Paste into Claude Code

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .claude/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/InternScience/scp/tree/main/skills/region-gene-elements

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/region-gene-elements .agents/skills/region-gene-elements && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .agents/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/region-gene-elements .cursor/skills/region-gene-elements && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .cursor/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/InternScience/scp.git --path skills/region-gene-elements

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/region-gene-elements .gemini/skills/region-gene-elements && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .gemini/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/region-gene-elements .github/skills/region-gene-elements && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .github/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill region-gene-elements -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install InternScience/scp region-gene-elements --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/region-gene-elements .opencode/skills/region-gene-elements && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "region-gene-elements" agent skill from https://github.com/InternScience/scp/tree/main/skills/region-gene-elements into .opencode/skills/region-gene-elements/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "region-gene-elements", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: region-gene-elements
GitHub stars: 169
Used in: 1 other repo
Token cost: ~747 tokens
SKILL.md length: 12 words
Files: 1
Skills in repo: 73
Repo updated: Jun 3, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

Tasks that involve Bioinformatics
Reaches api.catalogkg.igvf.org

What it does

Region Gene Elements is an agent skill from InternScience/scp. Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

Its SKILL.md is about 750 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

“/region-gene-elements”

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 tex and python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- api.catalogkg.igvf.org
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

Region Gene Elements loads about 747 tokens when it runs. Until then it costs about 43 tokens; SKILL.md has 12 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~43
When it runs · the whole SKILL.md, loaded when a task matches: ~747

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). 12 words, ~747 tokens.

Download SKILL.mdSave it as .claude/skills/region-gene-elements/SKILL.md (or your agent's skills folder).

name: region-gene-elements
description: Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.
license: MIT license
metadata.skill-author: PJLab

IGVF Catalog — Regulatory Element–Gene Associations by Region

Usage

Tool Description

tex

Query IGVF Catalog API to find regulatory-element-to-gene associations within a genomic region.
Database: IGVF Catalog (https://api.catalogkg.igvf.org/)
API: GET https://api.catalogkg.igvf.org/api/genomic-elements/genes

Args:
    region (str): Required. Genomic region, e.g. "chr1:903900-904900"
    organism (str): Default "Homo sapiens"
    source_annotation (str, optional): e.g. "enhancer", "intergenic"
    region_type (str, optional): e.g. "accessible dna elements", "tested elements"
    source (str, optional): e.g. "ENCODE_EpiRaction"
    method (str, optional): e.g. "CRISPR FACS screen"
    biosample_name (str, optional): e.g. "placenta"
    verbose (bool): true=返回完整信息, false=精简 (default false)
    page (int): 0-based page
    limit (int): 每页条目数, 最大 500

Return (list of dicts), each item contains:
    - score (float): 调控元件与基因的关联分数
    - source (str): 数据来源 (e.g. "ENCODE")
    - source_url (str): 来源链接
    - genomic_element (dict):
        - chr, start, end: 调控元件基因组坐标
        - source_annotation: 元件注释类型 (intergenic, enhancer, promoter 等)
        - type: 元件类型 (accessible dna elements, tested elements 等)
    - gene (dict):
        - _id: Ensembl Gene ID (e.g. "ENSG00000187634")
        - name: 基因名 (e.g. "SAMD11")
        - chr, start, end, strand: 基因坐标
        - gene_type: 基因类型 (protein_coding, lncRNA 等)
        - hgnc: HGNC ID (e.g. "HGNC:28706")
        - entrez: Entrez ID (e.g. "ENTREZ:148398")
    - biosample (str): 来源生物样本 (e.g. "natural killer cell...")
    - method (str): 实验方法 (e.g. "CRISPR FACS screen")

Query Example

python

import requests

region = "chr1:903900-904900"
url = "https://api.catalogkg.igvf.org/api/genomic-elements/genes"
params = {
    "region": region,
    "organism": "Homo sapiens",
    "verbose": "true",
    "page": 0,
}
resp = requests.get(url, params=params, timeout=30).json()

print(f"[IGVF] 区域 {region} 内调控元件-基因关联: {len(resp)} 条")

for i, item in enumerate(resp[:10]):
    gene = item.get("gene", {})
    elem = item.get("genomic_element", {})
    print(f"\n  [{i+1}] 基因: {gene.get('name', 'N/A')} ({gene.get('_id', '')})")
    print(f"       基因坐标: {gene.get('chr')}:{gene.get('start')}-{gene.get('end')} ({gene.get('strand')})")
    print(f"       基因类型: {gene.get('gene_type', '')}")
    print(f"       调控元件: {elem.get('chr')}:{elem.get('start')}-{elem.get('end')}")
    print(f"       元件类型: {elem.get('type', '')} ({elem.get('source_annotation', '')})")
    print(f"       关联分数: {item.get('score', 'N/A')}")
    print(f"       来源: {item.get('source', '')}, 方法: {item.get('method', '')}")
    print(f"       样本: {item.get('biosample', '')[:60]}")

Files

Just SKILL.md in skills/region-gene-elements 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

Region Gene Elements 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.

Region Gene Elements compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Region Gene Elements this skillInternScience/scp	169	1 repos	~747	Automated safety check: Pass	MIT	4 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	3 repos	~3.4k	Automated safety check: Notes	Apache-2.0	22 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	2 days ago
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	22 days ago
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw	15k	—	~923	Automated safety check: Pass	MIT	1 mo ago

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Questions about Region Gene Elements

What does Region Gene Elements do?

Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context. Region Gene Elements is an agent skill from InternScience/scp. Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

When should I use Region Gene Elements?

Region Gene Elements fits situations like: tasks that involve Bioinformatics.

How do I install Region Gene Elements in Claude Code?

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

How do I install Region Gene Elements in Codex?

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

Can I use Region Gene Elements 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 region-gene-elements -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/region-gene-elements, .gemini/skills/region-gene-elements, .github/skills/region-gene-elements and .opencode/skills/region-gene-elements in your project.

What does Region Gene Elements need to run?

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

Does Region Gene Elements access the network?

SKILL.md names 1 domain. In commands or code: api.catalogkg.igvf.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Region Gene Elements 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 Region Gene Elements use?

Region Gene Elements 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 Region Gene Elements use?

About 747 tokens (SKILL.md is roughly 3k 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 Region Gene Elements?

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

Who maintains Region Gene Elements?

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.

Region Gene Elements

Install Region Gene Elements

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

IGVF Catalog — Regulatory Element–Gene Associations by Region

Usage

Tool Description

Query Example

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

Dbsnp Database

Metabolic Study Planner

13C Metabolic Flux Analysis

Alphagenome Single Variant Analysis

MFA Pipeline Orchestrator

Singlecell Qc

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Questions about Region Gene Elements

Install Region Gene Elements

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

IGVF Catalog — Regulatory Element–Gene Associations by Region

Usage

Tool Description

Query Example

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from InternScience/scp

Related

Questions about Region Gene Elements