Scholar Open
joshzyj/open-scholar-skill
Implement open science practices for a social science study.
scPROTEIN 基于图神经网络，对单细胞蛋白组数据去批次效应降噪、不确定性估计、生成 embedding 与细胞类型表征，含 stage1/stage2 两子应用。
Install Scprotein Collection Skill
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install infometa/workbuddyskills scprotein-collection-skill --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .claude/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.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/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .claude/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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 install https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skillType 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.
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install infometa/workbuddyskills scprotein-collection-skill --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .agents/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .agents/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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.
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install infometa/workbuddyskills scprotein-collection-skill --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .cursor/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .cursor/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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 https://github.com/infometa/workbuddyskills.git --path experts/omics-scprotein-expert/skills/scprotein-collection-skill--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install infometa/workbuddyskills scprotein-collection-skill --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .gemini/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.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/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .gemini/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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.
$ gh skill install infometa/workbuddyskills scprotein-collection-skillInstalls 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).
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .github/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .github/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.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/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .github/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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.
$ npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install infometa/workbuddyskills scprotein-collection-skill --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/infometa/workbuddyskills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/experts/omics-scprotein-expert/skills/scprotein-collection-skill .opencode/skills/scprotein-collection-skill && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "scprotein-collection-skill" agent skill from https://github.com/infometa/workbuddyskills/tree/main/experts/omics-scprotein-expert/skills/scprotein-collection-skill into .opencode/skills/scprotein-collection-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scprotein-collection-skill", 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
scprotein-collection-skill- GitHub stars
- 348
- Token cost
- ~5k tokens
- SKILL.md length
- 942 words
- Files
- 8 (incl. scripts, references)
- Skills in repo
- 218
- Repo updated
- First seen
- Licence
- None found
At a glance
scPROTEIN 基于图神经网络，对单细胞蛋白组数据去批次效应降噪、不确定性估计、生成 embedding 与细胞类型表征，含 stage1/stage2 两子应用。
- Works in 8 steps: ：鉴权与配置双重检查 → ：登录授权 → ：配置引导 → …
- Tasks that involve Embeddings
- SKILL.md covers 合集锁定参数（SKILL 内部硬编码，禁止覆盖）, 子应用清单（硬编码 · 禁止运行时修改）, 能力边界 and 退出码 & 鉴权失败处理, plus 9 more sections
- Runs Python scripts from its folder; calls python3; reaches cloud.tencent.com
What it does
Scprotein Collection Skill is an agent skill from infometa/workbuddyskills. scPROTEIN 基于图神经网络，对单细胞蛋白组数据去批次效应降噪、不确定性估计、生成 embedding 与细胞类型表征，含 stage1/stage2 两子应用。
Its SKILL.md is about 5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including scripts and reference files (for example `CONTRACT.md`, `references/cli-whitelist.md` and `references/omics-cli-setup.md`).
It sits in AI & LLM Engineering, covering Embeddings and Reproducible research. It works with Nextflow. The repository describes itself as: WorkBuddy skills / connectors / experts archive for offline study.
When your agent uses it
- Tasks that involve Embeddings
- Tasks that involve Reproducible research
Example prompts
- “/scprotein-collection-skill”
Requirements
- Python 3
Workflow steps
8 steps, taken from the step headings in SKILL.md.
- ：鉴权与配置双重检查
- ：登录授权
- ：配置引导
- ：子应用选择（从硬编码清单中匹配，无需展开）
- ：运行前准备（必经）
- ：运行（仅形态 B · 公共应用）
- ：状态查询
- ：异步失败取证（debug 三段式）
What it can do on your machine
Read from SKILL.md and the folder at commit 91b77ea. 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
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python3
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:
cloud.tencent.com
Also links to:
console.cloud.tencent.comomics.qq.com
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
Scprotein Collection Skill loads about 5k tokens when it runs, and up to ~24k if it reads all its reference files. Until then it costs about 28 tokens; SKILL.md has 942 words of instructions outside code blocks.
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); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 942 words (~5,048 tokens).
- name
- scprotein-collection-skill
- triggers
- 图神经网络, scPROTEIN Collection (Nextflow), scprotein collection (nextflow), scprotein-collection-(nextflow), scprotein_collection_(nextflow)…
- platform
- 腾讯健康组学平台(Omics)
- tags
- 行业专业, 生信分析, 生物医药, omics, 腾讯健康组学平台, public-app, collection
- version
- 1.0.0
Files
SKILL.md and 7 other files (scripts, references) in experts/omics-scprotein-expert/skills/scprotein-collection-skill of infometa/workbuddyskills.
- SKILL.md
- CONTRACT.md
- references/cli-whitelist.md
- references/omics-cli-setup.md
- references/run-flow-spec.md
- references/runtime_error_kb.md
- references/skill-template.md
- scripts/omics_cli.py
Open the folder on GitHubat commit 91b77ea
Compare with similar skills
Scprotein Collection Skill 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Scprotein Collection Skill this skillinfometa/workbuddyskills | 348 | — | ~5k | Automated safety check: Pass | None | |
| Scholar Openjoshzyj/open-scholar-skill | 168 | — | ~14k | Automated safety check: Pass | Custom licence | |
| Chroma Vector DatabaseOrchestra-Research/AI-Research-SKILLs | 13k | 7 repos | ~2.3k | Automated safety check: Pass | MIT | |
| SageMaker Serving Image Selectionhuggingface/skills | 11k | 1 repos | ~4.6k | Automated safety check: Pass | Apache-2.0 | |
| Codebase Managementgiancarloerra/SocratiCode | 3.3k | 1 repos | ~1.8k | Automated safety check: Pass | AGPL-3.0 | |
| CLIP Image-Text MatchingOrchestra-Research/AI-Research-SKILLs | 13k | 7 repos | ~1.7k | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Scprotein Collection Skill
What does Scprotein Collection Skill do?
scPROTEIN 基于图神经网络，对单细胞蛋白组数据去批次效应降噪、不确定性估计、生成 embedding 与细胞类型表征，含 stage1/stage2 两子应用。. Scprotein Collection Skill is an agent skill from infometa/workbuddyskills.
When should I use Scprotein Collection Skill?
Scprotein Collection Skill fits situations like: tasks that involve Embeddings; tasks that involve Reproducible research.
How do I install Scprotein Collection Skill in Claude Code?
Run `npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a claude-code`. Or copy the skill folder (experts/omics-scprotein-expert/skills/scprotein-collection-skill in infometa/workbuddyskills) into .claude/skills/scprotein-collection-skill in your project. Claude Code loads it when a task matches its description.
How do I install Scprotein Collection Skill in Codex?
Run `npx skills add infometa/workbuddyskills --skill scprotein-collection-skill -a codex`. Or copy the skill folder (experts/omics-scprotein-expert/skills/scprotein-collection-skill in infometa/workbuddyskills) into .agents/skills/scprotein-collection-skill in your project. Codex loads it when a task matches its description.
Can I use Scprotein Collection Skill 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 infometa/workbuddyskills --skill scprotein-collection-skill -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scprotein-collection-skill, .gemini/skills/scprotein-collection-skill, .github/skills/scprotein-collection-skill and .opencode/skills/scprotein-collection-skill in your project.
What does Scprotein Collection Skill need to run?
Going by SKILL.md and its folder, Scprotein Collection Skill needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.
Does Scprotein Collection Skill access the network?
SKILL.md names 3 domains. In commands or code: cloud.tencent.com; the agent is likely to contact it when it follows the instructions. As links in the text: console.cloud.tencent.com and omics.qq.com. This is read from the text; nothing was executed.
Is Scprotein Collection Skill 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Scprotein Collection Skill use?
No licence was found for Scprotein Collection Skill or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Scprotein Collection Skill use?
About 5k tokens (SKILL.md is roughly 20k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 19k tokens, read only when the agent opens those files.
What are the alternatives to Scprotein Collection Skill?
Skills that share tags, products or a category with Scprotein Collection Skill: Scholar Open (joshzyj/open-scholar-skill, 168 stars), Chroma Vector Database (Orchestra-Research/AI-Research-SKILLs, 13k stars), SageMaker Serving Image Selection (huggingface/skills, 11k stars) and Codebase Management (giancarloerra/SocratiCode, 3.3k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Scprotein Collection Skill?
infometa (a GitHub user) maintains it in infometa/workbuddyskills, which has 348 GitHub stars. The repository holds 218 skills in this directory. The repository was last updated on October 9, 2026.
Source: infometa/workbuddyskills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.