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tooluniverse-rnaseq-deseq2

RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2 (default), edgeR (QL-F / exact test for small replicate counts), and limma-voom (large n / complex designs). Use when you have a count matrix + metadata, want to find DEGs, or need dispersion/PCA/clustering analysis. Includes RULE ZERO precedence (read executed.ipynb if present).

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# 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.