Agent skill

Replicate Paper

by brycewang-stanford in brycewang-stanford/Auto-Empirical-Research-Skills

Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report.

Custom licenceAuto-check: notesDocuments & Office

Install Replicate Paper

skills CLI

$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a claude-code

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

GitHub CLI

$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper --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/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .claude/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .claude/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper

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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a codex

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

GitHub CLI

$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .agents/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .agents/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a cursor

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

GitHub CLI

$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .cursor/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .cursor/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper

--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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a gemini-cli

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

GitHub CLI

$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper --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/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .gemini/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .gemini/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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 brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper

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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .github/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .github/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -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 brycewang-stanford/Auto-Empirical-Research-Skills replicate-paper --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper .opencode/skills/replicate-paper && 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 "replicate-paper" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper into .opencode/skills/replicate-paper/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "replicate-paper", 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: replicate-paper
GitHub stars: 4.5k
Token cost: ~1.9k tokens
SKILL.md length: 524 words
Files: 1
Skills in repo: 364
Repo updated: Oct 5, 2026
First seen: Oct 7, 2026
Licence: Custom licence

At a glance

Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report.

Works in 6 steps: Intake → Data Audit → Code Analysis → …
Asked to replicate a paper end-to-end
SKILL.md covers Invocation, The 6-Phase Pipeline, Quality Gate and Failure Modes & Recovery
Calls git and python

What it does

Replicate Paper is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report. Use when asked to replicate a paper end-to-end, or when invoked as /replicate-paper [paper.pdf] [data.csv|dta].

Its SKILL.md is about 1.9k 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 Documents & Office, covering Database administration, CSV and tabular files and PDF. It works with Python. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…

When your agent uses it

Asked to replicate a paper end-to-end
Invoked as /replicate-paper [paper.pdf] [data.csv|dta]

Example prompts

“/replicate-paper”

Requirements

Python 3
Pre-approved tools (allowed-tools): Read, Write, Edit, Bash, Glob, Grep

Workflow steps

6 steps, taken from the step headings in SKILL.md.

Intake
Data Audit
Code Analysis
Translation
Validation
Report

What it can do on your machine

Read from SKILL.md and the folder at commit 9fa87d8. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves these tools, so the agent can use them without asking each time:
- Read
- Write
- Edit
- Bash
- Glob
- Grep
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- git
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use git, which can reach the network depending on how they are called.
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

Replicate Paper loads about 1.9k tokens when it runs. Until then it costs about 79 tokens; SKILL.md has 524 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~79
When it runs · the whole SKILL.md, loaded when a task matches: ~1.9k

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: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
```
allowed-tools: Read, Write, Edit, Bash, Glob, Grep
```

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

Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 524 words (~1,888 tokens).

“Trigger: /replicate-paper [paper.pdf] [data.csv|dta] or "replicate this paper"”

— opening of SKILL.md by brycewang-stanford, Custom licence

name: replicate-paper
allowed-tools: Read, Write, Edit, Bash, Glob, Grep

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper of brycewang-stanford/Auto-Empirical-Research-Skills.

Open the folder on GitHubat commit 9fa87d8

Compare with similar skills

Replicate Paper 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.

Replicate Paper compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Replicate Paper this skillbrycewang-stanford/Auto-Empirical-Research-Skills	4.5k	—	~1.9k	Automated safety check: Notes	Custom licence	3 days ago
Instrument Data To Allotropeaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	2 repos	~2.7k	Automated safety check: Pass	Apache-2.0	7 days ago
Cc Streaming Export Safetydoccker/cc-use-exp	1.1k	—	~2.2k	Automated safety check: Pass	Custom licence	1 mo ago
Markdown Exporterbowenliang123/markdown-exporter	271	1 repos	~5.3k	Automated safety check: Pass	Apache-2.0	1 mo ago
Streaming Export Safetydoccker/cc-use-exp	1.1k	—	~1.9k	Automated safety check: Pass	Custom licence	1 mo ago
Vulnerability CSV Reportingbenchflow-ai/skillsbench	1.8k	—	~3k	Automated safety check: Pass	Apache-2.0	2 mo ago

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Works with

Python

Questions about Replicate Paper

What does Replicate Paper do?

Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report. Replicate Paper is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Run a full 6-phase autonomous replication of a biomedical/epidemiology paper against UK Biobank or similar cohort data, producing Python and R scripts plus a validated replication report.

When should I use Replicate Paper?

Replicate Paper fits situations like: asked to replicate a paper end-to-end; invoked as /replicate-paper [paper.pdf] [data.csv|dta].

How do I install Replicate Paper in Claude Code?

Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a claude-code`. Or copy the skill folder (skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/replicate-paper in your project. Claude Code loads it when a task matches its description.

How do I install Replicate Paper in Codex?

Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a codex`. Or copy the skill folder (skills/28-maxwell2732-paper-replicate-agent-demo/dot-claude/skills/replicate-paper in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/replicate-paper in your project. Codex loads it when a task matches its description.

Can I use Replicate Paper 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill replicate-paper -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/replicate-paper, .gemini/skills/replicate-paper, .github/skills/replicate-paper and .opencode/skills/replicate-paper in your project.

What does Replicate Paper need to run?

Going by SKILL.md and its folder, Replicate Paper needs the command-line tools its instructions call (git and python). Our summary lists: Python 3. Its frontmatter pre-approves these tools: Read, Write, Edit, Bash, Glob, Grep.

Does Replicate Paper access the network?

SKILL.md contains no URLs. Its commands use git, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Replicate Paper safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Replicate Paper use?

Replicate Paper has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.

How many tokens does Replicate Paper use?

About 1.9k tokens (SKILL.md is roughly 7.6k 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 Replicate Paper?

Skills that share tags, products or a category with Replicate Paper: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Cc Streaming Export Safety (doccker/cc-use-exp, 1.1k stars), Markdown Exporter (bowenliang123/markdown-exporter, 271 stars) and Streaming Export Safety (doccker/cc-use-exp, 1.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Replicate Paper?

brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,529 GitHub stars. The repository holds 364 skills in this directory. The repository was last updated on October 5, 2026.

Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Replicate Paper

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

Files

Compare with similar skills

Similar skills

More from brycewang-stanford/Auto-Empirical-Research-Skills

Related

Questions about Replicate Paper