RNA-seq Differential Expression Analysis (DESeq2) PRIMARY SCRIPTS — use these FIRST before writing custom code The four scripts below are deterministic, audited wrappers that handle the ambiguity in DESeq2 / correlation / PCA / ANOVA questions by emitting EVERY common interpretation in one call. Reading their output and matching the variant the published notebook used is more reliable than re-deriving the answer from scratch. All four scripts honor workspace isolation: they ONLY write to (or by default). They never touch the input data folder. Always pass when you need intermediate files. — R…