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factor-design-specification - Specify experimental design formula in DESeq2

Defines experimental design formulas in DESeq2 to model biological and technical factors explaining RNA-seq count variation.

Tags

Updated: 2026-09-18
transcriptomicsrnaseqdeseq2differential-expressionexperimental-design

Capabilities

Construct design formulasEncode batch effectsSpecify interaction termsSet factor reference levels

Typical Inputs

Count matrixSample column metadataDesign formula string

Typical Outputs

DESeqDataSet objectGLM coefficient estimatesDifferential expression results tables

What this skill does

  • Construct design formulas
  • Encode batch effects
  • Specify interaction terms
  • Set factor reference levels

Inputs

  • Count matrix
  • Sample column metadata
  • Design formula string

Outputs

  • DESeqDataSet object
  • GLM coefficient estimates
  • Differential expression results tables

Requirements

  • R environment
  • DESeq2 package

Source

  • Spec: SKILL.md

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