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Deseq2 differential expression

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/deseq2-differential-expression

DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualizationFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill deseq2-differential-expression

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SKILL.md

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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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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