Bulk RNA-seq Analysis Skill

This skill guides analysis of bulk RNA-seq gene expression count data using DESeq2, following established patterns from this project.

Quick Start

When asked to analyze RNA-seq data:

1. Check if a CLAUDE.md file exists in the study directory - it contains study-specific metadata
2. Determine the data format (count matrix, featureCounts output, RSEM, etc.)
3. Create numbered scripts in scripts/ directory (01_, 02_, etc.)
4. Update analysis.md after each analysis step
5. Generate all plots in results/plots/ with plots/plots.md documentation

Directory Structure

Create this structure for each analysis: