tooluniverse

tooluniverse is a Bioinformatics & life sciences skill for AI agents, published by mims-harvard in the ToolUniverse repository on GitHub. Skillspace rates tooluniverse D (68/100) and it passed the safety scan; the rating is based on static analysis only.

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square,…

Grade
D
Quality
68 / 100
Safety
Passed
GitHub stars
1,566

Unproven: rated by static analysis only, not yet compared head-to-head.

Our two independent classifiers differ on this skill's category, so treat the placement as provisional.

This rating describes the version of the repository we crawled; it may have changed since, so go by its current files.

View source on GitHubmims-harvard/ToolUniverse

Our review

Architecture
89 / 100
Maturity
Structured: ships references or scripts
Security scan
No issues found
License
Apache-2.0
Adoption
Adopted by 0 other repositories, in 2 collections

Not checked yet

  • Category is a classifier prediction; no model has read this skill 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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