deseq2-differential-expression
// DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization
$ git log --oneline --stat
stars:384
forks:73
updated:March 4, 2026
SKILL.mdreadonly
SKILL.md Frontmatter
namedeseq2-differential-expression
descriptionDESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization
allowed-toolsRead,Write,Glob,Grep,Edit,WebFetch,WebSearch,Bash
metadata[object Object]
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)