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scientific-packages/pydeseq2/SKILL.md
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@@ -7,15 +7,7 @@ description: "Differential gene expression analysis (Python DESeq2). Identify DE
## Overview
PyDESeq2 is a Python implementation of the DESeq2 method for differential expression analysis (DEA) with bulk RNA-seq data. This skill provides comprehensive support for designing and executing PyDESeq2 workflows, from data loading through result interpretation.
**Key capabilities:**
- Single-factor and multi-factor experimental designs
- Statistical testing using Wald tests with multiple testing correction
- Optional apeGLM log-fold-change shrinkage
- Data preprocessing and quality control
- Result export and visualization
- Integration with pandas, AnnData, and the Python data science ecosystem
PyDESeq2 is a Python implementation of DESeq2 for differential expression analysis with bulk RNA-seq data. Design and execute complete workflows from data loading through result interpretation, including single-factor and multi-factor designs, Wald tests with multiple testing correction, optional apeGLM shrinkage, and integration with pandas and AnnData.
## When to Use This Skill