PyDESeq2

Use this skill for bulk RNA-seq negative-binomial GLMs, with explicit biological replicates, covariates, and comparisons. Cells, sequencing lanes, and repeated measurements from the same donor are not independent biological replicates. Donor-level pseudobulk can be appropriate when its aggregation and design match the scientific question; this is not a single-cell per-cell testing workflow.

Current PyDESeq2 0.5.4 provides Wald tests and apeGLM-style coefficient shrinkage. Do not assume every feature or numerical result of current R DESeq2 is implemented identically. See API and tested versions for supported calls, AnnData storage, and source/runtime verification limits.

Analysis contract