{"slug":"k-dense-ai-bulk-rnaseq","source_name":"k-dense-ai/bulk-rnaseq","name":"K Dense AI/Bulk Rnaseq","description":"End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g. ","version":1,"lift":{"pass_rate_delta_pts":27.27,"pass_rate_pct":100,"total_cases":22,"passed_cases":22,"tokens_delta_pct":145,"turns_delta_pct":0,"verdict":"pass","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-07T15:42:38.525050+00:00"},"skill_score":1,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":27.27,"with_pass_pct":100,"without_pass_pct":72.7,"tokens_delta_pct":145,"turns_delta_pct":0,"total_cases":22,"cases_aggregated":22,"verdict":"pass","never_hurt":true,"completed_at":"2026-08-07T15:42:38.525050+00:00","run_id":"4a5a2e3c-68e7-4f30-bc07-394add02e8f8","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":"MIT","install_count":0,"manifest_hash":"db0554a942e6c72a3657c77ccb809fd54ac4585735adf0eb634413e5baa725da","raw_url":"https://app.decimal.ai/s/k-dense-ai-bulk-rnaseq/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/k-dense-ai-bulk-rnaseq"}