bulk-rnaseq
synthetic-sciences/openscienceSkill
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. "analyze my RNA-seq", "FASTQ to DESeq2", "run nf-core/rnaseq", "STAR/Salmon quantification", "build
Why this score
This repo hosts 10 skills, so its 4,120 stars are split between them (about 412 each) for scoring.
Popularity score: 75/100 from public GitHub signals only. It shows how widely used and maintained this is, not how well it works. Not included yet: the fake-star check. The security scan is shown separately and doesn't change the score. How we rank
Security
Scanned Oct 21, 2026 at commit 493f9261f94b, with Cisco's open-source skill-scanner.
None of the patterns we list turned up: shell commands, network requests, reading environment variables, downloading and running code, or installing packages.
A scan lists patterns in the code. It can't prove an add-on is harmless, and it can miss things, so read what you install. How we scan
Alternatives
Other makers' add-ons that do the same job, next to this one.
| Name | Score | Stars | Context | Updated |
|---|---|---|---|---|
| This onebulk-rnaseq synthetic-sciences/openscience · Skill | 75 | ★ 4.1k | ≈153 always | 17d ago |
| bulk-read ToolMonsters/claude-code-routing · Skill Both about bulk | 55 | ★ 24 | ≈76 always | 2mo ago |
| canvas-bulk-grading vishalsachdev/canvas-mcp · Skill Both about bulk | 66 | ★ 298 | ≈45 always | 16d ago |
| bulk-classify mrmps/classifier-dev · Skill Both about bulk | 64 | ★ 425 | ≈126 always | 17d ago |
| openspec-bulk-archive-change rivet-dev/rivet · Skill Both about bulk | 76 | ★ 6.3k | ≈29 always | 16d ago |