Claude Code CLI

AI-powered coding assistant for lab research

Read first: Staying in the Driver’s Seat — our guide to maintaining code ownership while using AI tools. Required reading for all lab members.

Read the Guide →

New to Claude Code? Follow our guided learning path to get up to speed quickly.

Start Learning Path →

Why Claude Code?

Claude Code is an AI-powered command-line tool that helps you write, understand, and debug code directly in your terminal. For Rashid Lab members, it offers:

Benefit How It Helps
Accelerate research Write code faster, debug quicker, automate repetitive tasks
Improve quality Built-in code review, catches common errors, enforces lab standards
Learning tool Ask Claude to explain code, methods, or statistical concepts
Integration Works with our existing git, targets, and HPC workflows
NoteLab Team Account

Rashid Lab has a Claude for Teams subscription. Contact Dr. Rashid to be added to the team account, which provides:

  • Shared usage across lab projects
  • No individual billing
  • Access to latest Claude models
TipWhere to Start

Most lab members only need the first three pages below: Installation, First Session, and Daily Workflow. The remaining pages are references you can consult as needed — you don’t need to read everything up front.

Quick Orientation

Topic Page Level You’ll Learn
Code Ownership Staying in the Driver’s Seat Essential Maintain understanding while using AI
Setup Installation Beginner Install locally and on Longleaf
Getting Started First Session Beginner Hands-on walkthrough with a real project
Daily Use Daily Workflow Intermediate Common patterns and best practices
Lab Tools Lab Integration Intermediate targets, git, Quarto, HPC integration
Longleaf HPC Usage Intermediate Running Claude on the cluster
Customization Advanced Advanced Skills, agents, hooks, global config
Help Troubleshooting — Common issues and solutions
Cheatsheet Reference — Quick command reference

How It Works

Claude Code runs in your terminal alongside your normal development workflow:

# Start Claude Code in any project directory
claude

# Claude sees your project files, git history, and CLAUDE.md instructions
# You chat naturally to explore, modify, and run code

Claude can:

  • Read and understand your entire codebase
  • Write and edit files directly
  • Run commands (git, Rscript, make, sbatch)
  • Explain code and help you learn
  • Review changes before committing

Lab-Specific Configuration

Every project in the lab uses a CLAUDE.md file that tells Claude about:

  • Project structure and purpose
  • Lab coding standards (base R + data.table, not tidyverse)
  • Common commands and workflows
  • Configuration files and their roles

This means Claude automatically follows lab conventions without you having to remind it.

Getting Started

Ready to start? Head to the Installation guide to set up Claude Code on your machine and Longleaf.

Already installed? Try the First Session walkthrough for a hands-on introduction.

Resources

Resource Link
Official Documentation claude.ai/code
Lab Handbook rashidlab.github.io/lab-handbook
GitHub Organization github.com/rashidlab
Claude for Teams claude.ai/team (PI access)