Agent-Skills.md

Agent Skills: DESeq2 Differential Expression Skill

DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization

bioinformaticsID: a5c-ai/babysitter/deseq2-differential-expression

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/deseq2-differential-expression

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/deseq2-differential-expression/SKILL.md

Skill Metadata

Name
deseq2-differential-expression
Description
DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization

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)