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creating-analysis-projects

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Scaffold clean, reproducible R pipelines.

Education & Research#single-cell RNA-seq#bioinformatics#reproducible research#directory conventions#R projects#pipeline scaffolding#Quarto QMD
Authorwolf5996
Version1.0.0
Installs0

System Documentation

What problem does it solve?

It solves the problem of messy, non-reproducible single-cell analysis projects by enforcing a strict directory architecture that cleanly separates version-controlled code from immutable inputs and generated outputs.

Core Features & Use Cases

  • Opinionated project scaffolding: Sets up a consistent read/, scripts/, checkpoints/, write/ triad and validates that pipelines follow it.
  • Pipeline-ready conventions: Enforces numbered QMD notebooks, shared utils.R, flat checkpoints/ handoffs, and per-notebook output provenance under write/figures/ and write/tables/.
  • Tooling integration for AI agents: Requires using writing-r-code for R generation and writing-qmd-scientific for scientific Quarto structure, plus higher-level planning superpowers for multi-notebook pipelines.

Quick Start

Ask the AI to scaffold a new single-cell RNA-seq analysis project that follows the read → scripts → checkpoints → write conventions.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: creating-analysis-projects
Download link: https://github.com/wolf5996/agentic-skills/archive/main.zip#creating-analysis-projects

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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