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 --workdir (or /tmp/... by default). They never touch the input data folder. Always pass --workdir /tmp/<run-name> when you need intermediate files.