Deseq2 Differential Expression
by a5c-ai
DESeq2 differential expression analysis skill with normalization, statistical modeling, and visualization
Skill Details
Repository Files
1 file in this skill directory
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)
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