pydeseq2

SKILL.md

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.

For users who want to perform a standard differential expression analysis:

Important: Shrinkage affects only the log2FoldChange values, not the statistical test results (p-values remain unchanged). Use shrunk values for visualization but report unshrunken p-values for significance.

Analyse différentielle de l'expression génique (Python DESeq2). Identifiez les gènes DE à partir de décomptes massifs d’ARN-seq, de tests de Wald, de correction FDR, de tracés volcan/MA, pour l’analyse d’ARN-seq. Source : jackspace/claudeskillz.

Voir l'original