rnaseq-analysis
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:
- Check if a
CLAUDE.mdfile exists in the study directory - it contains study-specific metadata - Determine the data format (count matrix, featureCounts output, RSEM, etc.)
- Create numbered scripts in
scripts/directory (01_, 02_, etc.) - Update
analysis.mdafter each analysis step - Generate all plots in
results/plots/withplots/plots.mddocumentation
Directory Structure
Create this structure for each analysis:
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