DESeq2 Differential Expression Skill

Purpose

Provide DESeq2 differential expression analysis with normalization, statistical modeling, and visualization.

Capabilities

• Size factor normalization
• Negative binomial modeling
• Shrinkage estimation
• Batch effect modeling
• Multi-factor designs
• Result visualization (MA plots, volcano plots)

Usage Guidelines

• Design experiments with appropriate replication
• Include batch effects in model when present
• Apply appropriate shrinkage estimators
• Use multiple testing correction
• Generate publication-quality visualizations
• Document analysis parameters and thresholds

Dependencies

• DESeq2
• edgeR
• limma-voom

Process Integration

• RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
• Single-Cell RNA-seq Analysis (scrnaseq-analysis)
• CRISPR Screen Analysis (crispr-screen-analysis)