{"slug":"mims-harvard-tooluniverse-rnaseq-deseq2","source_name":"mims-harvard/tooluniverse-rnaseq-deseq2","name":"Mims Harvard/Tooluniverse Rnaseq Deseq2","description":"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 (r","version":1,"lift":{"pass_rate_delta_pts":13.64,"pass_rate_pct":63.6,"total_cases":22,"passed_cases":14,"tokens_delta_pct":462.7,"turns_delta_pct":0,"verdict":"mixed","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-06T15:10:56.938148+00:00"},"skill_score":0.6364,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":13.64,"with_pass_pct":63.6,"without_pass_pct":50,"tokens_delta_pct":462.7,"turns_delta_pct":0,"total_cases":22,"cases_aggregated":19,"verdict":"mixed","never_hurt":false,"completed_at":"2026-08-06T15:10:56.938148+00:00","run_id":"8d70e48d-48d4-4882-a466-64087a57d63c","version_number":1,"is_latest_version":true,"gate":null}],"trust":{"skill_safety":"passed","safety_status":"clean","intent_verdict":"safe","content_status":"clean","indexable":true},"license":"Apache-2.0","install_count":0,"manifest_hash":"4baeaaea4f345d28a2558ae75469d49d60fcebe5c5c44f097f0f13dc109752d9","raw_url":"https://app.decimal.ai/s/mims-harvard-tooluniverse-rnaseq-deseq2/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/mims-harvard-tooluniverse-rnaseq-deseq2"}