AzureML Project Scaffolding
Kilo-Org/kilo-marketplace
Sets up and maintains AzureML-ready Python projects as uv workspaces with devcontainers, a Makefile and job YAML, so local runs match cloud jobs and experiments stay reproducible.
Scaffold a new research project with full reproducibility infrastructure in R and/or Python.
Install Research Init
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills research-init --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/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/61-phdemotions-research-methods/skills/research-init .claude/skills/research-init && 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 "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .claude/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-initType 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills research-init --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ 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/61-phdemotions-research-methods/skills/research-init .agents/skills/research-init && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .agents/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills research-init --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ 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/61-phdemotions-research-methods/skills/research-init .cursor/skills/research-init && 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 "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .cursor/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/61-phdemotions-research-methods/skills/research-init--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 brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills research-init --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ 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/61-phdemotions-research-methods/skills/research-init .gemini/skills/research-init && 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 "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .gemini/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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 brycewang-stanford/Auto-Empirical-Research-Skills research-initInstalls 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ 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/61-phdemotions-research-methods/skills/research-init .github/skills/research-init && 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 "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .github/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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 brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills research-init --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ 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/61-phdemotions-research-methods/skills/research-init .opencode/skills/research-init && 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 "research-init" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/61-phdemotions-research-methods/skills/research-init into .opencode/skills/research-init/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-init", 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
research-init- GitHub stars
- 4.5k
- Token cost
- ~839 tokens
- SKILL.md length
- 356 words
- Files
- 14 (incl. references)
- Skills in repo
- 364
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Scaffold a new research project with full reproducibility infrastructure in R and/or Python.
- Works in 6 steps: Gather requirements → Create directory structure → Initialize environments → …
- The user says new project
- SKILL.md covers How to scaffold a project, Principles, Voice and Argument handling
- Runs R and Python scripts from its folder; calls git
What it does
Research Init is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Scaffold a new research project with full reproducibility infrastructure in R and/or Python. Creates directory structure, pipeline stubs (targets/Snakemake), environment lockfiles (renv/uv), documentation templates (codebook, decision log, pre-registration, Cornell README), Quarto manuscript template, and proper .gitignore. Can wrap existing data in gold-standard structure. Use when the user says "new project," "scaffold," "start a study," "set up a project," "I have data and need to organize it," or when…
Its SKILL.md is about 840 tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files, including reference files (for example `references/criteria.md`, `references/principles.md` and `references/templates/decision.md`).
It sits in Development, covering Project scaffolding, Reproducible research and Dependency management. It works with Python and Git. 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
- The user says new project
- Set up a project
- I have data and need to organize it
- /research-intake recommends scaffolding
Example prompts
- “new project,”
- “scaffold,”
- “start a study,”
- “/research-init”
Requirements
- Python 3
Workflow steps
6 steps, taken from the step headings in SKILL.md.
- Gather requirements
- Create directory structure
- Initialize environments
- Handle existing data
- Initialize git
- Print summary and next steps
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 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 script files (R and Python), which the agent can run.
Shell commands in SKILL.md call:
git
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
Research Init loads about 839 tokens when it runs, and up to ~8.2k if it reads all its reference files. Until then it costs about 141 tokens; SKILL.md has 356 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); 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 356 words (~839 tokens).
“You create the structure that makes everything else possible. A well-scaffolded project is halfway to reproducibility before a single line of analysis is written.”
- name
- research-init
- argument-hint
- <project name> [--lang r|python|both] [--existing-data <path>]
Files
SKILL.md and 13 other files (references) in skills/61-phdemotions-research-methods/skills/research-init of brycewang-stanford/Auto-Empirical-Research-Skills.
- SKILL.md
- references/criteria.md
- references/principles.md
- references/templates/citation.cff
- references/templates/decision.md
- references/templates/gitignore
- references/templates/manuscript.qmd
- references/templates/pipeline-status.md
- references/templates/pre-registration.md
- references/templates/readme.md
- references/templates/setup.R
- references/templates/setup.py
- references/templates/snakefile
- references/templates/targets.R
Open the folder on GitHubat commit 9fa87d8
Compare with similar skills
Research Init 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 |
|---|---|---|---|---|---|---|
| Research Init this skillbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~839 | Automated safety check: Pass | Custom licence | |
| AzureML Project ScaffoldingKilo-Org/kilo-marketplace | 190 | — | ~3.1k | Automated safety check: Notes | MIT | |
| Light Project StructureLight0305/Light-skills | 641 | — | ~3k | Automated safety check: Notes | MIT | |
| Python Packagingwshobson/agents | 40k | 12 repos | ~911 | Automated safety check: Pass | MIT | |
| Rocky Codegenrocky-data/rocky | 304 | — | ~1.9k | Automated safety check: Pass | Apache-2.0 | |
| Modern Python ToolchainXiaomiMiMo/MiMo-Code | 14k | — | ~1.5k | Automated safety check: Notes | MIT |
Similar skills
Light Project Structure
Light0305/Light-skills
Audits, scaffolds and safely migrates research project folder structures, keeping existing repositories read-only until you approve exact moves from a plan.
Python Packaging
wshobson/agents
Package and publish Python libraries and CLI tools: project layout, pyproject.toml, build backends, wheels and source distributions, versioning and PyPI releases.
Rocky Codegen
rocky-data/rocky
Rocky CLI JSON-output schema cascade. An agent skill from rocky-data/rocky.
Modern Python Toolchain
XiaomiMiMo/MiMo-Code
Sets up Python projects with uv for packages and environments, ruff for linting and formatting, and pyright for type checking, with rules for running everything through uv.
Audit AI Code
jxnl/personal-monorepo-template
Audit, de-slop, parameterize, modularize, or safely clean up AI-generated or AI-shaped backend/general code.
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Related
Categories
Questions about Research Init
What does Research Init do?
Scaffold a new research project with full reproducibility infrastructure in R and/or Python. Research Init is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Scaffold a new research project with full reproducibility infrastructure in R and/or Python.
When should I use Research Init?
Research Init fits situations like: the user says new project; set up a project; I have data and need to organize it; /research-intake recommends scaffolding.
How do I install Research Init in Claude Code?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a claude-code`. Or copy the skill folder (skills/61-phdemotions-research-methods/skills/research-init in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/research-init in your project. Claude Code loads it when a task matches its description.
How do I install Research Init in Codex?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill research-init -a codex`. Or copy the skill folder (skills/61-phdemotions-research-methods/skills/research-init in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/research-init in your project. Codex loads it when a task matches its description.
Can I use Research Init 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 research-init -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/research-init, .gemini/skills/research-init, .github/skills/research-init and .opencode/skills/research-init in your project.
What does Research Init need to run?
Going by SKILL.md and its folder, Research Init needs R and Python for the scripts in its folder and the command-line tools its instructions call (git). Our summary lists: Python 3.
Does Research Init 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 Research Init 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 Research Init use?
Research Init 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 Research Init use?
About 839 tokens (SKILL.md is roughly 3.4k 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 7.3k tokens, read only when the agent opens those files.
What are the alternatives to Research Init?
Skills that share tags, products or a category with Research Init: AzureML Project Scaffolding (Kilo-Org/kilo-marketplace, 190 stars), Light Project Structure (Light0305/Light-skills, 641 stars), Python Packaging (wshobson/agents, 40k stars) and Rocky Codegen (rocky-data/rocky, 304 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Research Init?
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.