Claude Code Setup Guide

node --version

npm install -g @anthropic-ai/claude-code

claude --version

cd ~/your-research-project
claude

# Research Project: AI in Education

## Project Goal
Analyze the impact of AI tools on student learning outcomes through
literature synthesis and empirical analysis.

## File Structure
- /literature/ - Curated papers in markdown format
- /analysis/ - Data files and R scripts
- /drafts/ - Paper sections and outlines
- /exports/ - Final outputs (PDF, Word)

## Research Protocol
- Citation style: APA 7th Edition
- Inclusion criteria: Peer-reviewed, 2020-2025, empirical studies
- Analysis approach: Thematic synthesis

## Custom Commands
- /summarize: Create structured summary of a paper
- /compare: Compare methodologies across papers
- /synthesize: Identify themes across multiple papers

"Summarize the key arguments in @/literature/smith2024.md"

"Compare the methodologies in @/literature/jones2024.md
and @/literature/lee2024.md"

"Analyze all papers in @/literature/ and identify common themes"

mkdir -p .claude/commands

Summarize the following paper in this exact structure:

Paper: $ARGUMENTS

## Summary Template
- **Research Question**: [What problem does it address?]
- **Methodology**: [How did they study it?]
- **Key Findings**: [What did they discover?]
- **Theoretical Contribution**: [What does it add to knowledge?]
- **Limitations**: [What are the gaps?]
- **Relevance**: [How does this relate to my research?]

Be specific and cite page numbers where relevant.

claude  # Launch Claude Code

/summarize @/literature/smith2024.md

Compare these two papers systematically:

Papers: $ARGUMENTS

## Comparison Framework
1. **Research Questions**: How do they differ?
2. **Methodologies**: Qualitative vs quantitative? Samples?
3. **Findings**: Do they agree or contradict?
4. **Theories**: What frameworks do they use?
5. **Gaps**: What does each paper miss that the other addresses?

Present in a comparison table.

Analyze the following papers for research gaps:

Papers: $ARGUMENTS

## Gap Analysis
1. **Methodological Gaps**: What methods are missing?
2. **Theoretical Gaps**: What theories are underexplored?
3. **Empirical Gaps**: What contexts are understudied?
4. **Temporal Gaps**: What recent developments aren't covered?

For each gap, explain why it matters and what research it suggests.

/Your-Research-Project/
├── CLAUDE.md                 # Project memory
├── .claude/
│   └── commands/             # Custom slash commands
├── literature/               # Curated papers (markdown)
├── analysis/                 # Data, scripts, results
├── notes/                    # Research notes, synthesis
├── drafts/                   # Paper sections
└── exports/                  # Final outputs

Create a research project structure with folders for literature,
analysis, notes, drafts, and exports. Then create a CLAUDE.md file
documenting this project structure.

mkdir -p literature analysis notes drafts exports .claude/commands
touch CLAUDE.md
claude

Read @/literature/smith2024.md and create a structured summary
following the format in CLAUDE.md

Compare the methodologies in @/literature/smith2024.md,
@/literature/jones2024.md, and @/literature/lee2024.md.
Create a comparison table.

Analyze all papers in @/literature/ and identify the 3 most
common themes. For each theme, list which papers discuss it
and how their perspectives differ.

Review all files in @/literature/ and organize them into
subfolders by research method (qualitative, quantitative, mixed-methods)

Extract the following from each paper in @/literature/:
author, year, method, sample size, key finding.
Create a CSV table with this data.

Based on the papers in @/literature/, create an outline for
a literature review section covering theoretical frameworks.

Using the synthesis notes in @/notes/themes.md, draft a
2-page literature review section in academic style (APA 7th).

# Literature Analysis Project

## Goal
Analyze papers on [TOPIC] to identify themes, methodologies, and gaps.

## File Structure
- /literature/ - Papers in markdown format
- /synthesis/ - Theme notes and comparisons
- /outputs/ - Final analysis documents

## Analysis Protocol
- Extract: Research question, method, key findings
- Compare: Methodologies and theoretical frameworks
- Synthesize: Common themes and research gaps

Analyze this paper:

Paper: $ARGUMENTS

Extract:
1. Research question and objectives
2. Methodology (qualitative/quantitative/mixed)
3. Sample and data collection
4. Key findings (3-5 bullet points)
5. Theoretical contribution
6. Limitations and future research

Format as markdown table for easy compilation.

1. /analyze @/literature/paper1.md
2. /analyze @/literature/paper2.md
3. /analyze @/literature/paper3.md

Then: "Create a comparison table of the three analyses above,
focusing on methodological differences."

Using Sequential Thinking, analyze the papers in @/literature/
and propose a novel theoretical framework that integrates their
key findings. Work step-by-step through:
1. Identifying core constructs
2. Mapping relationships
3. Proposing mechanisms
4. Identifying testable propositions

"Use 3 parallel agents to analyze @/literature/smith2024.md:
- Agent 1: Focus on methodology quality
- Agent 2: Focus on theoretical contribution
- Agent 3: Focus on practical implications

Compare their assessments."

"Create a Git commit for the changes we just made with
message: 'Add literature analysis for Smith 2024'"

"Show me the diff of changes since yesterday"

"Create a new branch for the theory-building section"

"Create a todo list for analyzing these 10 papers:
- Read and summarize each
- Extract methodologies
- Identify common themes
- Map theoretical frameworks
- Draft synthesis section"

/code "Analyze @/data/interview1.md using thematic analysis.
Identify codes, group into themes, provide exemplar quotes."

"Using Sequential Thinking MCP, develop a theoretical model
that integrates findings from @/synthesis/themes.md.
Work through: constructs → relationships → propositions → testable hypotheses."