name: deseq2-differential-expression description: DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • transcriptomics
  • differential-expression
  • statistics
  • rna-seq

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)