# Hex Research

Keeps a research graph of hypotheses, goals, runs, source quality and audits. Useful when you need to remember why a conclusion exists.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed · ★ 583
- Author: levnikolaevich
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/levnikolaevich/claude-code-skills
- Updated: 2026-10-18
- HTML: https://affpapa.org/en/nevibecode/mcp/hex-research

## What it does

Hex Research is an MCP server that stores research as a graph. Hypotheses, goals, runs, source quality scoring, audits and generated maps all live in one structure instead of scattered notes.

It runs through `npx`, so there is no separate service to host. Claude accepts two names: `claude mcp add hex-research-mcp -- npx -y @levnikolaevich/hex-research-mcp` or `claude mcp add hex-research -- npx -y @levnikolaevich/hex-research-mcp`. Codex takes a single line: `codex mcp add hex-research -- npx -y @levnikolaevich/hex-research-mcp`. Cursor and GitHub Copilot are configured with a JSON block holding `command` and `args`, while Gemini CLI uses `gemini mcp add hex-research npx -y @levnikolaevich/hex-research-mcp`.

Node.js has to be present in your environment, because the server starts via `npx`. Supported clients are Claude, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline and Zed.

## Requirements
- Needs: Node.js (commands run via npx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add hex-research-mcp -- npx -y @levnikolaevich/hex-research-mcp
```

### Codex

**Platform CLI**
```bash
codex mcp add hex-research -- npx -y @levnikolaevich/hex-research-mcp
```

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "hex-research": {
            "command": "npx",
            "args": [
                "-y",
                "@levnikolaevich/hex-research-mcp"
            ]
        }
    }
}
```

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "hex-research": {
            "type": "stdio",
            "command": "npx",
            "args": [
                "-y",
                "@levnikolaevich/hex-research-mcp"
            ]
        }
    }
}
```

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add hex-research npx -y @levnikolaevich/hex-research-mcp
```

## When to use it
- keep hypotheses and goals in one graph instead of loose notes
- trace which runs confirmed or killed a hypothesis
- score source quality before relying on a source
- audit a research effort and spot the gaps
- generate a map of the research from collected data

## Example prompts
- Add a hypothesis about the checkout conversion drop and link it to a research goal
- Show which runs support this hypothesis and flag the weak sources
- Generate a research map across all goals and runs

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