Agent skill

Scientific Pkg Gget

ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。

Install Scientific Pkg Gget

skills CLI

$ npx skills add affaan-m/ECC --skill scientific-pkg-gget -a claude-code

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

GitHub CLI

$ gh skill install affaan-m/ECC scientific-pkg-gget --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/affaan-m/ECC.git skills-src && mkdir -p .claude/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .claude/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .claude/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget

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 affaan-m/ECC --skill scientific-pkg-gget -a codex

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

GitHub CLI

$ gh skill install affaan-m/ECC scientific-pkg-gget --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .agents/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .agents/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .agents/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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 affaan-m/ECC --skill scientific-pkg-gget -a cursor

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

GitHub CLI

$ gh skill install affaan-m/ECC scientific-pkg-gget --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .cursor/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .cursor/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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/affaan-m/ECC.git --path docs/ja-JP/skills/scientific-pkg-gget

--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 affaan-m/ECC --skill scientific-pkg-gget -a gemini-cli

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

GitHub CLI

$ gh skill install affaan-m/ECC scientific-pkg-gget --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/affaan-m/ECC.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .gemini/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .gemini/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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 affaan-m/ECC scientific-pkg-gget

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 affaan-m/ECC --skill scientific-pkg-gget -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .github/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .github/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .github/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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 affaan-m/ECC --skill scientific-pkg-gget -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 affaan-m/ECC scientific-pkg-gget --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/docs/ja-JP/skills/scientific-pkg-gget .opencode/skills/scientific-pkg-gget && 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 "scientific-pkg-gget" agent skill from https://github.com/affaan-m/ECC/tree/main/docs/ja-JP/skills/scientific-pkg-gget into .opencode/skills/scientific-pkg-gget/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-pkg-gget", 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: scientific-pkg-gget
GitHub stars: 276k
Token cost: ~870 tokens
SKILL.md length: 145 words
Files: 1
Skills in repo: 683
Repo updated: Oct 10, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Works in 5 steps: 必要な種、アセンブリ、遺伝子 ID タイプ、データベースを特定する。 → 引数に関する現在のモジュールドキュメントを確認する。 → まず小さなクエリを実行する。 → …
Research & Science work in your project
SKILL.md covers 使用するタイミング, インストール, 基本パターン and 主要なモジュール, plus 4 more sections
Calls python and uv

What it does

Scientific Pkg Gget is an agent skill from affaan-m/ECC. ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。

Its SKILL.md is about 870 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. It works with Python and Ensembl. The repository describes itself as: The agent harness performance optimization system. Skills, instincts, memory, security, and research-first development for Claude Code, Codex, Opencode, Cursor and beyond. The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/scientific-pkg-gget”

Requirements

Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

必要な種、アセンブリ、遺伝子 ID タイプ、データベースを特定する。
引数に関する現在のモジュールドキュメントを確認する。
まず小さなクエリを実行する。
明示的なファイル名と日付で出力を保存する。
モジュール名、バージョン、引数、データベースの前提条件を記録する。

What it can do on your machine

Read from SKILL.md and the folder at commit 4eb71d9. 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
Shell commands in SKILL.md call:
- python
- uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- pachterlab.github.io
- github.com
- doi.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

Scientific Pkg Gget loads about 870 tokens when it runs. Until then it costs about 32 tokens; SKILL.md has 145 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~32
When it runs · the whole SKILL.md, loaded when a task matches: ~870

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 affaan-m/ECC at commit 4eb71d9, republished under its MIT licence (© affaan-m). 145 words, ~870 tokens.

Download SKILL.mdSave it as .claude/skills/scientific-pkg-gget/SKILL.md (or your agent's skills folder).

name: scientific-pkg-gget
description: ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。
origin: community

gget

gget CLI または Python パッケージを使用してゲノム参照データベースにわたるクイックバイオインフォマティクス検索が必要なタスクにこのスキルを使用します。

使用するタイミング

Ensembl ID、遺伝子メタデータ、転写産物の詳細、または配列の検索。
フルローカルパイプラインを構築せずにクイックな BLAST または BLAT 検索を実行。
Ensembl から参照ゲノムリンクとアノテーションを取得。
単一のインターフェースを通してタンパク質構造、パスウェイ、がん、発現、または疾患関連モジュールを照会。
Biopython、Snakemake、Nextflow、BLAST+、またはデータベース固有のクライアントなどの重いツールに移行する前に再現可能な最初の証拠ログを作成。

タスクが規制対象の臨床解釈、高スループット本番パイプライン、またはデータベースバージョンとローカルインデックスの細かい制御を必要とする場合は、gget の代わりに専用のワークフローを使用します。

インストール

クリーンな Python 環境を使用します。

bash

python -m venv .venv
. .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install --upgrade gget
gget --help

uv が利用可能な場合:

bash

uv venv
. .venv/bin/activate
uv pip install gget

古い環境を使用する前に、gget をアップグレードしてモジュールドキュメントを再確認します。gget が照会するアップストリームデータベースは時間とともに変化します。

基本パターン

CLI の形式:

bash

gget <module> [arguments] [options]

Python の形式:

python

import gget

result = gget.search(["BRCA1"], species="human")
print(result)

一般的なワークフロー:

必要な種、アセンブリ、遺伝子 ID タイプ、データベースを特定する。
引数に関する現在のモジュールドキュメントを確認する。
まず小さなクエリを実行する。
明示的なファイル名と日付で出力を保存する。
モジュール名、バージョン、引数、データベースの前提条件を記録する。

主要なモジュール

正確な引数については現在のアップストリームドキュメントを使用してください。これらのモジュールは一般的な最初の選択肢です:

gget search: 検索語から Ensembl ID を検索。
gget info: Ensembl、UniProt、または関連 ID のメタデータを取得。
gget seq: ヌクレオチドまたはアミノ酸配列を取得。
gget ref: 参照ゲノムのダウンロードリンクを取得。
gget blast: クイック BLAST クエリを実行。
gget blat: サポートされているゲノムアセンブリに対して配列を配置。
gget muscle: 多重配列アライメントを実行。
gget diamond: 参照配列に対してローカル配列アライメントを実行。
gget alphafold と gget pdb: タンパク質構造参照を調べる。
gget enrichr、gget opentargets、gget archs4、gget bgee、gget cbio、gget cosmic: エンリッチメント、ターゲット、発現、がん、疾患関連データを探索。

すべてのモジュールがすべての Python バージョンまたは依存関係セットをサポートするとは限りません。一部のオプションの科学的依存関係は、コアパッケージよりも狭いバージョンサポートを持ちます。

クイック例

遺伝子を検索:

bash

gget search -s human brca1 dna repair -o brca1-search.json

遺伝子メタデータを取得:

bash

gget info ENSG00000012048 -o brca1-info.json

配列を取得:

bash

gget seq ENSG00000012048 -o brca1-seq.fa

小さな BLAST クエリを実行:

bash

gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json

Python の例:

python

import gget

genes = gget.search(["BRCA1", "DNA repair"], species="human")
info = gget.info(["ENSG00000012048"])
sequence = gget.seq("ENSG00000012048")

再現性ログ

科学的な出力については、クエリを再現するのに十分なメタデータを含めます。

markdown

| 日付 | gget バージョン | モジュール | クエリ | 種/アセンブリ | 出力 | 注記 |
| --- | --- | --- | --- | --- | --- | --- |
| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | 実行前にドキュメントを確認 |

以下も記録します:

Python バージョンと環境マネージャー。
gget setup を通してインストールされたオプションの依存関係。
クエリによって返されたデータベース固有の識別子。
出力が JSON、CSV、FASTA、または DataFrame エクスポートのいずれであるか。
gget のアップグレードで解決された障害。

レビューチェックリスト

インストールされた gget バージョンをアップグレードまたは確認したか？
引数を使用する前に現在のアップストリームモジュールドキュメントを確認したか？
種またはアセンブリは明示的か？
Ensembl/UniProt プレフィックスを含む識別子は正確に保存されているか？
結果は臨床解釈ではなくデータベース出力としてラベル付けされているか？
保存されたコマンドまたは Python スニペットからクエリを再現できるか？
オプションの依存関係は隔離された環境にインストールされているか？

参考文献

Files

Just SKILL.md in docs/ja-JP/skills/scientific-pkg-gget of affaan-m/ECC.

Open the folder on GitHubat commit 4eb71d9

Compare with similar skills

Scientific Pkg Gget 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.

Scientific Pkg Gget compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Scientific Pkg Gget this skillaffaan-m/ECC	276k	—	~870	Automated safety check: Pass	MIT	yesterday
Ggetdavila7/claude-code-templates	33k	10 repos	~6.3k	Automated safety check: Pass	MIT	today
Bio Biomart QueriesGPTomics/bioSkills	1.2k	2 repos	~3.2k	Automated safety check: Pass	MIT	1 mo ago
Tooluniverse Epigenomicswu-yc/LabClaw	1.1k	2 repos	~14k	Automated safety check: Pass	None	6 mo ago
Ggetaipoch/medical-research-skills	1.9k	—	~816	Automated safety check: Pass	MIT	24 days ago
Gget Genomic Databasesjaechang-hits/SciAgent-Skills	374	2 repos	~5.3k	Automated safety check: Pass	BSD-2-Clause	12 days ago

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Questions about Scientific Pkg Gget

What does Scientific Pkg Gget do?

ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。. Scientific Pkg Gget is an agent skill from affaan-m/ECC.

When should I use Scientific Pkg Gget?

Scientific Pkg Gget fits situations like: research & Science work in your project.

How do I install Scientific Pkg Gget in Claude Code?

Run `npx skills add affaan-m/ECC --skill scientific-pkg-gget -a claude-code`. Or copy the skill folder (docs/ja-JP/skills/scientific-pkg-gget in affaan-m/ECC) into .claude/skills/scientific-pkg-gget in your project. Claude Code loads it when a task matches its description.

How do I install Scientific Pkg Gget in Codex?

Run `npx skills add affaan-m/ECC --skill scientific-pkg-gget -a codex`. Or copy the skill folder (docs/ja-JP/skills/scientific-pkg-gget in affaan-m/ECC) into .agents/skills/scientific-pkg-gget in your project. Codex loads it when a task matches its description.

Can I use Scientific Pkg Gget 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 affaan-m/ECC --skill scientific-pkg-gget -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scientific-pkg-gget, .gemini/skills/scientific-pkg-gget, .github/skills/scientific-pkg-gget and .opencode/skills/scientific-pkg-gget in your project.

What does Scientific Pkg Gget need to run?

Going by SKILL.md and its folder, Scientific Pkg Gget needs the command-line tools its instructions call (python and uv). Our summary lists: Python 3.

Does Scientific Pkg Gget access the network?

SKILL.md names 3 domains. As links in the text: pachterlab.github.io, github.com and doi.org. This is read from the text; nothing was executed.

Is Scientific Pkg Gget 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 Scientific Pkg Gget use?

Scientific Pkg Gget is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Scientific Pkg Gget use?

About 870 tokens (SKILL.md is roughly 3.5k 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 Scientific Pkg Gget?

Skills that share tags, products or a category with Scientific Pkg Gget: Gget (davila7/claude-code-templates, 33k stars), Bio Biomart Queries (GPTomics/bioSkills, 1.2k stars), Tooluniverse Epigenomics (wu-yc/LabClaw, 1.1k stars) and Gget (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Scientific Pkg Gget?

affaan-m (a GitHub user) maintains it in affaan-m/ECC, which has 276,111 GitHub stars. The repository holds 683 skills in this directory. The repository was last updated on October 10, 2026.

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

Install Scientific Pkg Gget

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

gget

使用するタイミング

インストール

基本パターン

主要なモジュール

クイック例

再現性ログ

レビューチェックリスト

参考文献

Files

Compare with similar skills

Similar skills

More from affaan-m/ECC

Related

Questions about Scientific Pkg Gget