Skill UI

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

PyDESeq2 is a robust Python implementation for conducting differential gene expression analysis on bulk RNA-seq count data. It supports complete statistical workflows, including data loading from various formats, complex multi-factor design specifications (e.g., accounting for batch effects or covariates), normalization, and performing advanced Wald tests. It is ideal for researchers transitioning R-based DESeq2 analyses into scalable Python pipelines.

This skill provides an end-to-end, highly reproducible workflow for bulk RNA-seq differential expression analysis. It orchestrates the entire pipeline, guiding users from raw FASTQ reads through Quality Control (QC), trimming, alignment (STAR/Salmon), quantification, generating a gene-level counts matrix, and finally executing differential expression testing (pydeseq2) and pathway enrichment analysis. It is designed for robust, statistically sound, and fully documented results.