Research Kit

Deep Research Toolkit for AI Agents

An open source toolkit for conducting structured, rigorous research with AI agents. Move beyond ad-hoc queries to systematic investigation with quality standards and reproducible methodologies.

Origin & Motivation

Research Kit is a fork of Spec Kit by GitHub, originally built as a personal project to adapt the Specification-Driven Development (SDD) workflow for systematic research.

The deeper motivation behind this project is to demonstrate a simple but powerful idea: AI agents perform significantly better when guided by multiple structured phases and template constraints. Instead of asking an AI to "do research" in a single open-ended prompt, Research Kit breaks the process into 10 distinct phases, each with its own template, quality standards, and output expectations. This structured approach:

Reduces hallucination by constraining AI output to specific, well-defined templates at each phase
Improves consistency by enforcing the same methodology across different research topics
Enables quality control by making each phase reviewable before proceeding to the next
Produces better results by giving the AI clear context boundaries instead of unbounded instructions

If you've ever noticed that AI gives better answers when you break a complex question into smaller parts, Research Kit applies that principle systematically to the entire research workflow.

For details on what changed from the upstream Spec Kit, see The Fork.

What is Research Kit?

Research Kit is a structured research framework designed for AI agents. It transforms ad-hoc prompting into systematic investigation by providing:

Multi-phase research workflow - From defining research questions to executing comprehensive studies
Quality standards enforcement - Built-in principles for source evaluation, methodology rigor, and bias mitigation
Research type specialization - Tailored approaches for academic, market, technical, and general research
Reproducible methodologies - Documented approaches that can be validated and replicated
Citation management - Integrated BibTeX support for proper source attribution
AI agent integration - Works with Claude Code and Codex CLI

The Problem

Traditional AI interactions treat research as a single-shot query: you ask a question, get an answer, and hope it's accurate. This approach struggles with:

Lack of source transparency - Where did this information come from?
No methodology documentation - How was this answer derived?
Inconsistent quality - Results vary wildly between queries
No bias mitigation - Unexamined assumptions baked into responses
Poor reproducibility - Can't validate or build on previous research

Research Kit solves this by making research a structured, auditable process rather than a black-box interaction.

Who It's For

Research Kit is designed for anyone who needs rigorous, documented research:

Researchers & Academics - Literature reviews, hypothesis exploration, methodology design
Business Analysts - Market research, competitive analysis, trend investigation
Technical Writers - Technology evaluations, framework comparisons, best practices documentation
Consultants - Client research, industry analysis, strategic recommendations
Students - Term papers, thesis research, learning new domains
Product Managers - User research synthesis, feature validation, market positioning

If you need defensible conclusions backed by documented sources and transparent methodology, Research Kit is for you.

Key Features

Structured Research Workflow

Research Kit guides you through a systematic 10-phase process:

Principles - Establish research quality standards and ethical guidelines
Define - Articulate research questions, objectives, and scope
Refine - Clarify ambiguities and sharpen focus (optional)
Methodology - Design research approach and data collection strategy
Validate - Review feasibility and identify potential issues (optional)
Tasks - Break down research into executable activities
Execute - Conduct research and collect data
Analyze - Process data and generate statistical insights
Synthesize - Draw conclusions and answer research questions
Publish - Create publication-ready outputs (reports, papers, presentations)

Multiple Research Types

Specialized templates and guidance for different research domains:

Academic Research - Literature reviews, peer-reviewed sources, scholarly rigor
Market/Business Research - Industry analysis, competitive intelligence, market trends
Technical Research - Technology evaluations, architecture decisions, implementation strategies
General Investigation - Open-ended exploration, cross-domain synthesis, curiosity-driven inquiry

Research Quality Standards

Built-in enforcement of research best practices:

Source Quality - Distinction between primary/secondary sources, peer review status, recency
Methodology Rigor - Explicit research design, assumption documentation, limitation acknowledgment
Ethics & Bias - Conflict of interest disclosure, bias mitigation, diverse perspective inclusion
Citation Standards - Proper attribution with BibTeX format, source accessibility
Analysis Quality - Transparent frameworks, data interpretation rationale, alternative explanations
Report Completeness - Executive summaries, methodology sections, supported findings, justified conclusions

AI Agent Compatibility

Works seamlessly with popular AI coding agents through slash commands and structured prompts.

Research Agents

In addition to slash commands, Research Kit provides custom agents for autonomous multi-step workflows:

Agent	Purpose	When to Use
agent-research-assistant	Full SRD workflow orchestrator	Starting new research, guided workflow
agent-research-reviewer	Quality assurance specialist	Validating research, checking rigor
agent-literature-specialist	Literature review expert	Conducting systematic literature reviews, source evaluation
agent-analysis-expert	Data analysis specialist	Statistical analysis, visualization, pattern discovery
agent-data-collector	Data collection specialist	Web scraping, API integration, systematic data gathering
agent-academic-writer	Academic writing specialist	Creating publication-ready research outputs

Agent Invocation:

Use @agent-name syntax to invoke a specific agent (e.g., @agent-research-reviewer)
Agents have specialized knowledge and tools for their domain
Slash commands suggest relevant agents at completion (e.g., "ask @agent-research-reviewer to validate the definition")

Agents vs Slash Commands:

Agents have isolated context and handle complex multi-step workflows autonomously
Slash commands are lightweight utilities for single-step tasks within your main conversation

Agents are deployed to agent-specific locations (e.g., .claude/agents/) and can be invoked using @agent-name mentions.

Quick Start

1. Install Research CLI

Choose your preferred installation method:

Option 1: Persistent Installation (Recommended)

Install once and use everywhere:

uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

Then use the tool directly:

research init my-research-project
research check

To upgrade:

uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

Option 2: One-time Usage

Run directly without installing:

uvx --from git+https://github.com/nguyenvanduocit/research-kit.git research init my-research-project

2. Establish Research Principles

Launch your AI assistant in the project directory. The /research.* commands are available.

Use the /research.principles command to establish your research quality standards:

/research.principles Create principles focused on academic rigor, peer-reviewed sources, bias mitigation, and transparent methodology. Include ethical guidelines for data handling and citation standards.

3. Define Research Question

Use the /research.define command to articulate what you want to investigate:

/research.define I need to understand the current state of AI agent frameworks for software development. What are the leading approaches, their strengths/weaknesses, adoption trends, and future directions? Target audience is engineering leadership making tooling decisions.

4. Design Research Methodology

Use the /research.methodology command to plan your research approach:

/research.methodology Conduct academic research focused on peer-reviewed papers, industry reports, and framework documentation. Include quantitative analysis of GitHub stars/activity and qualitative assessment of architectural patterns. Timeline: 2 weeks.

5. Break Down Research Tasks

Use /research.tasks to create an actionable research plan:

/research.tasks

6. Execute Research

Use the following commands to conduct and complete your research:

/research.execute    # Collect data and conduct research
/research.analyze    # Analyze collected data
/research.synthesize # Draw conclusions from findings
/research.publish    # Create final research outputs

Research Workflow

Research Kit implements a structured 10-phase workflow designed to ensure quality, reproducibility, and defensibility:

Phase 1: Principles - Establish Research Standards

Define the quality standards that will govern your research:

Source evaluation criteria (peer review, primary vs secondary, recency)
Methodology requirements (rigor, documentation, limitations)
Ethical guidelines (bias mitigation, conflicts of interest, diverse perspectives)
Citation standards (format, attribution, accessibility)
Analysis frameworks (interpretation rules, confidence levels, alternative explanations)
Report requirements (structure, completeness, justification standards)

Output: /principles/research-principles.md

Phase 2: Define - Articulate Research Questions

Clearly state what you're investigating and why:

Primary research question and sub-questions
Research objectives and success criteria
Scope and boundaries (what's included/excluded)
Target audience and intended use
Background context and motivation
Key terms and definitions

Output: /research/<research-id>/definition.md

Phase 3: Refine - Clarify Scope (Optional)

Interactive clarification to address ambiguities:

Structured questioning to identify underspecified areas
Scope refinement and boundary clarification
Assumption surfacing and validation
Stakeholder alignment on research direction

Output: Updates to definition.md with Clarifications section

Phase 4: Methodology - Design Research Approach

Plan how you'll conduct the research:

Research type selection (academic, market, technical, general)
Data collection strategy (sources, search terms, inclusion/exclusion criteria)
Analysis framework (how you'll synthesize findings)
Timeline and milestones
Resource requirements
Quality assurance approach

Output: /research/<research-id>/methodology.md

Phase 5: Validate - Review Feasibility (Optional)

Check for potential issues before investing effort:

Source availability and accessibility
Timeline realism
Resource constraint validation
Methodology soundness review
Bias and blind spot identification

Output: Updates to methodology.md with Validation section

Phase 6: Tasks - Break Down Activities

Convert methodology into executable steps:

Literature search tasks (by domain, source type, time period)
Data collection activities (interviews, surveys, experiments)
Analysis tasks (coding, synthesis, pattern identification)
Writing tasks (sections, drafts, reviews)
Dependency mapping and parallel work identification

Output: /research/<research-id>/tasks.md

Phase 7: Execute - Conduct Research & Collect Data

Execute the research methodology to gather data:

Implement data collection protocols
Conduct experiments or surveys as designed
Gather literature and documentary evidence
Record observations systematically
Track execution progress and deviations
Maintain data quality and integrity

Output: /research/<research-id>/execution.md, /research/<research-id>/data/, /research/<research-id>/logs/

Phase 8: Analyze - Process Data & Generate Insights

Analyze collected data using appropriate methods:

Clean and prepare data for analysis
Apply statistical tests and models
Generate visualizations and figures
Identify patterns and relationships
Compare findings with literature
Document all analysis decisions

Output: /research/<research-id>/analysis.md, /research/<research-id>/figures/, /research/<research-id>/tables/

Phase 9: Synthesize - Draw Conclusions

Integrate findings to answer research questions:

Connect findings to research questions
Identify emergent themes and patterns
Build theoretical contributions
Develop practical implications
Assess confidence in conclusions
Acknowledge limitations honestly

Output: /research/<research-id>/synthesis.md, /research/<research-id>/models/

Phase 10: Publish - Create Publication Outputs

Transform research into publication-ready formats:

Generate comprehensive research reports
Create academic papers for journals
Develop presentations for stakeholders
Write executive briefs for decision-makers
Format citations and bibliographies
Prepare submission packages

Output: /research/<research-id>/publications/, /research/<research-id>/bibliography.bib

Research Types

Research Kit supports four specialized research approaches:

Academic Research

Focus: Scholarly rigor, peer-reviewed sources, theoretical frameworks

Best For:

Literature reviews
Theory development
Hypothesis testing
Academic paper preparation
Systematic reviews

Standards:

Prioritize peer-reviewed journals and academic presses
Document search strategies (databases, terms, filters)
Use established analytical frameworks (PRISMA, etc.)
Comprehensive citation with DOIs
Acknowledge limitations and future research directions

Market/Business Research

Focus: Industry trends, competitive analysis, business intelligence

Best For:

Market opportunity assessment
Competitive landscape mapping
Customer research synthesis
Strategic decision support
Investment due diligence

Standards:

Balance authoritative sources (industry reports, financial data) with emerging signals (news, social media)
Triangulate findings across multiple source types
Distinguish fact from opinion/projection
Consider source incentives and potential bias
Include both quantitative metrics and qualitative insights

Technical Research

Focus: Technology evaluation, implementation strategies, architecture decisions

Best For:

Framework/library comparisons
Architecture pattern evaluation
Tool selection decisions
Best practices documentation
Technology trend analysis

Standards:

Prioritize official documentation and maintainer guidance
Include hands-on testing or proof-of-concept validation
Document version specificity and compatibility
Assess community health and long-term viability
Consider maintenance burden and total cost of ownership

General Investigation

Focus: Open-ended exploration, cross-domain synthesis, curiosity-driven inquiry

Best For:

Learning new domains
Exploratory research without fixed hypothesis
Connecting disparate topics
Building mental models
Answering complex "why" or "how" questions

Standards:

Start broad, narrow based on findings
Document reasoning for source selection and synthesis
Acknowledge uncertainty and confidence levels
Seek diverse perspectives explicitly
Build clear narrative from evidence to conclusions

Supported AI Agents

Research Kit is optimized for CLI-based AI agents:

Agent	Support	Notes
Claude Code	✅	Full support with agents and commands
Codex CLI	✅	Full research workflow support

Installation

Requirements

Linux/macOS/Windows
uv for package management
Python 3.11+
Supported AI agent
Git (optional, for version control)

Install with uv (Recommended)

# Persistent installation
uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

# Verify installation
research check

Install with pip

pip install git+https://github.com/nguyenvanduocit/research-kit.git

Upgrade

# With uv
uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

# With pip
pip install --upgrade git+https://github.com/nguyenvanduocit/research-kit.git

Research CLI Reference

The research command supports the following options:

Commands

Command	Description
`init`	Initialize a new Research Kit project from the latest template
`check`	Check for installed tools and AI agents

`research init` Arguments & Options

Argument/Option	Type	Description
`<project-name>`	Argument	Name for your new research project directory (optional if using `--here`, or use `.` for current directory)
`--ai`	Option	AI assistant to use: `claude` or `codex`
`--ignore-agent-tools`	Flag	Skip checks for AI agent tools
`--no-git`	Flag	Skip git repository initialization
`--here`	Flag	Initialize project in the current directory instead of creating a new one
`--force`	Flag	Force merge/overwrite when initializing in current directory (skip confirmation)
`--skip-tls`	Flag	Skip SSL/TLS verification (not recommended)
`--debug`	Flag	Enable detailed debug output for troubleshooting
`--github-token`	Option	GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)

Examples

# Basic project initialization
research init literature-review

# Initialize with Claude Code
research init market-analysis --ai claude

# Initialize with Codex CLI
research init tech-evaluation --ai codex

# Initialize in current directory
research init . --ai claude
# or use the --here flag
research init --here --ai codex

# Force merge into current (non-empty) directory
research init . --force --ai claude

# Skip git initialization
research init my-research --ai codex --no-git

# Enable debug output
research init my-research --ai claude --debug

# Use GitHub token for API requests
research init my-research --ai claude --github-token ghp_your_token_here

# Check system requirements
research check

Available Slash Commands

After running research init, your AI agent will have access to these research commands:

Core Research Commands

Essential commands for the Research Kit workflow:

Command	Description
`/research.principles`	Create or update research quality standards and ethical guidelines
`/research.define`	Define research question, objectives, and scope
`/research.methodology`	Design research approach and data collection strategy
`/research.tasks`	Generate actionable research task breakdown
`/research.execute`	Conduct research and collect data systematically
`/research.analyze`	Analyze collected data and generate insights
`/research.synthesize`	Synthesize findings and draw conclusions
`/research.publish`	Create publication-ready outputs (reports, papers, presentations)

Optional Research Commands

Additional commands for enhanced research quality:

Command	Description
`/research.refine`	Clarify underspecified areas (recommended before `/research.methodology`)
`/research.validate`	Review methodology feasibility and identify potential issues (run after `/research.methodology`, before `/research.tasks`)
`/research.quality`	Generate custom quality checklists for research validation

Environment Variables

Variable	Description
`RESEARCH_ID`	Override research ID detection for non-Git repositories. Set to the research directory name (e.g., `001-ai-agent-frameworks`) to work on a specific research project when not using Git branches.

Example Output

A completed research project generates the following structure:

my-research-project/
├── principles/
│   └── research-principles.md        # Quality standards and ethical guidelines
├── research/
│   └── 001-ai-agent-frameworks/      # Research project directory
│       ├── definition.md             # Research question and scope
│       ├── methodology.md            # Research approach and strategy
│       ├── tasks.md                  # Actionable research breakdown
│       ├── execution.md              # Research execution log
│       ├── analysis.md               # Data analysis and insights
│       ├── synthesis.md              # Conclusions and findings
│       ├── publications/             # Publication-ready outputs
│       │   ├── report.md             # Comprehensive research report
│       │   ├── paper.md              # Academic paper (if applicable)
│       │   └── presentation.md       # Executive presentation
│       ├── data/                     # Collected research data
│       ├── figures/                  # Charts and visualizations
│       ├── tables/                   # Data tables
│       └── bibliography.bib          # BibTeX citation database
└── templates/
    ├── definition-template.md        # Template for new research questions
    ├── methodology-template.md       # Template for research approaches
    ├── tasks-template.md             # Template for task breakdowns
    └── report-template.md            # Template for research reports

Sample Report Structure

Research reports follow a standardized structure for clarity and reproducibility:

# Research Report: AI Agent Frameworks for Software Development

## Executive Summary
High-level findings, key conclusions, actionable recommendations (2-3 paragraphs)

## Research Question & Objectives
- Primary question: What are the leading AI agent frameworks for software development?
- Sub-questions: Strengths/weaknesses, adoption trends, future directions
- Success criteria: Comprehensive landscape mapping with actionable recommendations

## Methodology
- Research type: Technical Research
- Sources: Academic papers (10), industry reports (5), framework docs (15), GitHub metrics
- Search strategy: Google Scholar, arXiv, GitHub trending, Stack Overflow surveys
- Analysis framework: Comparative evaluation matrix (features, adoption, maturity, ecosystem)
- Timeline: 2 weeks (Jan 15 - Jan 29, 2025)

## Findings
### Theme 1: Framework Architecture Patterns
- Evidence from sources [1], [3], [7]
- Key insight: Three dominant patterns (agentic, workflow-based, hybrid)
- Supporting data: GitHub star trends, adoption curves

### Theme 2: Adoption Drivers
- Evidence from sources [2], [5], [9]
- Key insight: Developer experience beats raw capability in adoption

[Additional themes...]

## Analysis
- Cross-theme patterns and tensions
- Alternative interpretations considered
- Confidence levels and uncertainty acknowledgment
- Implications for engineering leadership

## Conclusions
- Direct answers to research questions
- Actionable recommendations
- Limitations and caveats
- Future research directions

## References
[1] Smith, J. et al. (2024). "Agentic AI Frameworks: A Survey." Journal of Software Engineering...
[2] Chen, L. (2024). "State of AI Development Tools 2024." Industry Report...
[Full BibTeX in bibliography.bib]

Documentation

Complete Research-Driven Investigation Methodology - Deep dive into the research process
Agent Integration Guide - Integration instructions and agent development guide
Contributing Guide - How to contribute to Research Kit
Support Resources - Getting help and reporting issues

Prerequisites

Before using Research Kit, ensure you have:

Operating System: Linux, macOS, or Windows
Python: Version 3.11 or higher (download)
Package Manager: uv (recommended) or pip
AI Agent: One of the supported AI coding agents
Git (optional): For version control and branch-based research organization

Most users will have Python and pip already installed. To install uv:

# macOS/Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows
powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Troubleshooting

Git Credential Manager on Linux

If you're having issues with Git authentication on Linux, install Git Credential Manager:

#!/usr/bin/env bash
set -e
echo "Downloading Git Credential Manager v2.6.1..."
wget https://github.com/git-ecosystem/git-credential-manager/releases/download/v2.6.1/gcm-linux_amd64.2.6.1.deb
echo "Installing Git Credential Manager..."
sudo dpkg -i gcm-linux_amd64.2.6.1.deb
echo "Configuring Git to use GCM..."
git config --global credential.helper manager
echo "Cleaning up..."
rm gcm-linux_amd64.2.6.1.deb

SSL/TLS Certificate Issues

If you encounter SSL certificate errors (common in corporate environments):

# Temporary workaround (not recommended for production)
research init my-project --skip-tls

# Better solution: Install certificates
# macOS
pip install certifi

# Linux
sudo apt-get install ca-certificates

Command Not Found After Installation

If research command is not found after installation:

# Check uv tool installation
uv tool list

# Reinstall with explicit path
uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

# Verify PATH includes uv tools directory
echo $PATH | grep -q ".local/bin" || echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

Agent Not Detected

If the CLI doesn't detect your AI agent:

# Check if agent is in PATH
which claude     # or codex

# Skip agent check and install anyway
research init my-project --ignore-agent-tools --ai claude

For More Help

Contributing

We welcome contributions to Research Kit! Here's how you can help:

Ways to Contribute

Report bugs - Found something broken? Open an issue
Suggest features - Have ideas for new research types or workflow improvements? We'd love to hear them
Improve documentation - Help make Research Kit easier to use
Add agent support - Integrate new AI coding agents
Enhance templates - Improve research templates and quality standards
Share research examples - Contribute example research projects

Getting Started

Read the Contributing Guide
Check the Code of Conduct
Look for "good first issue" labels
Fork the repository and make your changes
Submit a pull request

Development Setup

# Clone the repository
git clone https://github.com/nguyenvanduocit/research-kit.git
cd research-kit

# Install dependencies with uv
uv sync

# Run the CLI locally
uv run research --help

# Test your changes
uv run research init test-project --ai claude

For detailed development instructions, see CONTRIBUTING.md.

License

This project is licensed under the terms of the MIT open source license. Please refer to the LICENSE file for the full terms.

Acknowledgements

Research Kit is a fork of Spec Kit by GitHub. The original project focuses on Specification-Driven Development (SDD) for software engineering. Research Kit adapts the same multi-phase, template-constrained approach for systematic research workflows.

Special thanks to the GitHub team for creating Spec Kit and demonstrating that structured constraints make AI agents dramatically more effective.

Start conducting rigorous, reproducible research with AI agents today.
uv tool install research-cli --force --from git+https://github.com/nguyenvanduocit/research-kit.git

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.github		.github
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memory		memory
scripts/bash		scripts/bash
src/research_cli		src/research_cli
templates		templates
.gitattributes		.gitattributes
.gitignore		.gitignore
.markdownlint-cli2.jsonc		.markdownlint-cli2.jsonc
AGENTS.md		AGENTS.md
CHANGELOG.md		CHANGELOG.md
CLAUDE.md		CLAUDE.md
CODE_OF_CONDUCT.md		CODE_OF_CONDUCT.md
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
README.md		README.md
SECURITY.md		SECURITY.md
SUPPORT.md		SUPPORT.md
pyproject.toml		pyproject.toml
research-driven.md		research-driven.md

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Research Kit

Deep Research Toolkit for AI Agents

Origin & Motivation

Table of Contents

What is Research Kit?

The Problem

Who It's For

Key Features

Structured Research Workflow

Multiple Research Types

Research Quality Standards

AI Agent Compatibility

Research Agents

Quick Start

1. Install Research CLI

Option 1: Persistent Installation (Recommended)

Option 2: One-time Usage

2. Establish Research Principles

3. Define Research Question

4. Design Research Methodology

5. Break Down Research Tasks

6. Execute Research

Research Workflow

Phase 1: Principles - Establish Research Standards

Phase 2: Define - Articulate Research Questions

Phase 3: Refine - Clarify Scope (Optional)

Phase 4: Methodology - Design Research Approach

Phase 5: Validate - Review Feasibility (Optional)

Phase 6: Tasks - Break Down Activities

Phase 7: Execute - Conduct Research & Collect Data

Phase 8: Analyze - Process Data & Generate Insights

Phase 9: Synthesize - Draw Conclusions

Phase 10: Publish - Create Publication Outputs

Research Types

Academic Research

Market/Business Research

Technical Research

General Investigation

Supported AI Agents

Installation

Requirements

Install with uv (Recommended)

Install with pip

Upgrade

Research CLI Reference

Commands

research init Arguments & Options

Examples

Available Slash Commands

Core Research Commands

Optional Research Commands

Environment Variables

Example Output

Sample Report Structure

Documentation

Prerequisites

Troubleshooting

Git Credential Manager on Linux

SSL/TLS Certificate Issues

Command Not Found After Installation

Agent Not Detected

For More Help

Contributing

Ways to Contribute

Getting Started

Development Setup

License

Acknowledgements

About

Resources

License

Code of conduct

Contributing

Security policy

Uh oh!

Stars

`research init` Arguments & Options

Packages