decoupler
decoupler is a Bioinformatics & life sciences skill for AI agents, published by scverse in the decoupler repository on GitHub. Skillspace rates decoupler C (71/100) and it passed the safety scan; the rating is based on static analysis only.
Use for any task involving the decoupler library — inferring biological activity/enrichment scores from omics data (bulk, single-cell, spatial). Triggers on estimating transcription factor (TF) activity, pathway activity, or gene-set enrichment from an AnnData/DataFrame; running ulm, mlm, ora, gsea, gsva, aucell, viper, zscore, waggr, mdt, udt; multi-method consensus; fetching prior knowledge (CollecTRI, DoRothEA, PROGENy, MSigDB hallmarks, OmniPath); pseudobulk and expression filtering; using bundled example datasets (pbmc3k, covid5k, erygast1k, hsctgfb, msvisium, knocktf, toy) and whether they are raw counts or normalized; ranking/plotting activity scores; or benchmarking methods against ground truth. This is a router skill — read the relevant file under references/ before writing decoupler code, because outputs land in different places and several defaults are non-obvious.
- Grade
- C
- Quality
- 71 / 100
- Safety
- Passed
- GitHub stars
- 281
Unproven: rated by static analysis only, not yet compared head-to-head.
This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.
Our review
- Architecture
- 94 / 100
- Maturity
- Structured: ships references or scripts
- Security scan
- No issues found
- License
- BSD-3-Clause
- Adoption
- Adopted by 0 other repositories, in 0 collections
Not checked yet
- Not judged on the rubric yet (not a contender in its category)
- No blind task eval yet
- Scope (portable / vendor / repo-internal) not assessed; only the top of each category is read for scope
- Sibling files (scripts, references) not fetched; security scan covers SKILL.md only
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