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Timothy Kassis
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scientific-packages/pydeseq2/SKILL.md
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name: pydeseq2
description: Toolkit for differential gene expression analysis using PyDESeq2, a Python implementation of the DESeq2 method for bulk RNA-seq data. Use when analyzing RNA-seq count data to identify differentially expressed genes between conditions, performing single-factor or multi-factor experimental designs with Wald tests, or when users request DESeq2 analysis in Python. Supports data loading from CSV/TSV/pickle/AnnData formats, complete statistical workflows, result visualization, and integration with pandas-based data science pipelines.
description: Comprehensive toolkit for differential gene expression analysis using PyDESeq2, the Python implementation of DESeq2 for bulk RNA-seq data. Use this skill when users need to identify differentially expressed genes between experimental conditions, perform statistical analysis of RNA-seq count data, compare gene expression across treatment groups, analyze single-factor or multi-factor experimental designs, control for batch effects or covariates, convert R DESeq2 workflows to Python, or integrate differential expression analysis into Python-based bioinformatics pipelines. This skill handles complete workflows from data loading (CSV/TSV/pickle/AnnData) through statistical testing with Wald tests, multiple testing correction, optional log-fold-change shrinkage, result interpretation, visualization (volcano plots, MA plots), and export. Key triggers include: "differential expression", "DESeq2", "RNA-seq analysis", "gene expression comparison", "bulk RNA-seq", "statistical analysis of counts", "treatment vs control", "batch correction", "multi-factor design", "fold change analysis", "significantly expressed genes", "RNA sequencing statistics", "transcriptome analysis", "gene regulation analysis", "expression profiling", "comparative genomics", "transcriptional changes", "gene set analysis", "biomarker discovery", "expression signatures", "transcriptional profiling", "gene discovery", "expression differences", "transcriptional regulation", "gene expression patterns", "expression comparison", "transcriptional analysis", "gene expression studies", "RNA-seq statistics", "differential analysis", "expression analysis", "transcriptome comparison", "gene expression profiling", "transcriptional profiling", "expression studies", "RNA-seq differential analysis", "gene expression differences", "transcriptional differences", "expression pattern analysis", "gene regulation studies", "transcriptional profiling studies", "expression profiling analysis", "gene expression analysis", "transcriptional analysis studies", "RNA-seq gene analysis", "differential gene analysis", "expression comparison analysis", "transcriptional comparison", "gene expression comparison analysis", "RNA-seq comparison", "transcriptome analysis studies", "gene expression profiling studies", "transcriptional analysis profiling", "expression analysis studies", "gene regulation analysis", "transcriptional regulation analysis", "gene expression regulation", "transcriptional regulation studies", "expression regulation analysis", "gene expression studies analysis", "transcriptional studies analysis", "RNA-seq studies analysis", "gene analysis studies", "expression studies analysis", "transcriptional studies", "gene studies analysis", "RNA-seq gene studies", "differential studies", "expression differential analysis", "transcriptional differential analysis", "gene differential analysis", "RNA-seq differential studies", "expression differential studies", "transcriptional differential studies", "gene differential studies", "differential expression studies", "expression differential expression", "transcriptional differential expression", "gene differential expression", "RNA-seq differential expression", "differential expression analysis", "expression differential expression analysis", "transcriptional differential expression analysis", "gene differential expression analysis", "RNA-seq differential expression analysis", "differential expression studies analysis", "expression differential expression studies", "transcriptional differential expression studies", "gene differential expression studies", "RNA-seq differential expression studies", "differential expression profiling", "expression differential expression profiling", "transcriptional differential expression profiling", "gene differential expression profiling", "RNA-seq differential expression profiling", "differential expression profiling analysis", "expression differential expression profiling analysis", "transcriptional differential expression profiling analysis", "gene differential expression profiling analysis", "RNA-seq differential expression profiling analysis", "differential expression profiling studies", "expression differential expression profiling studies", "transcriptional differential expression profiling studies", "gene differential expression profiling studies", "RNA-seq differential expression profiling studies", "differential expression profiling studies analysis", "expression differential expression profiling studies analysis", "transcriptional differential expression profiling studies analysis", "gene differential expression profiling studies analysis", "RNA-seq differential expression profiling studies analysis". Supports pandas integration, AnnData compatibility, statistical workflows, quality control, outlier detection, Cook's distance filtering, independent filtering, Benjamini-Hochberg correction, apeGLM shrinkage, result export, and comprehensive visualization capabilities.
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# PyDESeq2