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CC tooluniverse-gene-enrichment

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 13 files · 2 scripts body ≈ 3 777 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

As a process C 58/100 · Has gaps — References files that are not bundled: ../tooluniverse-network-pharmacology/SKILL.md, ../tooluniverse-multiomic-disease-characterization/SKILL.md, ../tooluniverse-spatial-omics-analysis/SKILL.md

AnalyzerData and analyticsSoftware developmentWriting and documentstype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
C
87/100
safety, quality, tests
Safety 60%
90
Quality 40%
83
Run on models
none yet
Process rating
C
58/100
Has gaps
References files that are not bundled: ../tooluniverse-network-pharmacology/SKILL.md, ../tooluniverse-multiomic-disease-characterization/SKILL.md, ../tooluniverse-spatial-omics-analysis/SKILL.md
Tools and files w 18
0
Result and completion w 14
0
Progress reporting w 2
0
the three weakest of ten parameters · all ten

How to improve

  1. The text references files that are not there: add them or drop the references.
For the model run — optional
  • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
  • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

Guard findings · 10

✓ No critical or high findings

Medium and low: 10
  • low Secrets in code secret-high-entropy-token references/enrichr_guide.md:152
    High-entropy token-like string (may be an id, hash or a credential) (detector / deny-list definition)
    - `Desc…021` - Human developmental cell types
    detector
  • low Secrets in code secret-high-entropy-token references/enrichr_guide.md:153
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `Alle…021` - Brain cell types
    quoted
  • low Secrets in code secret-high-entropy-token references/enrichr_guide.md:177
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `TRRU…019` - Human TF regulatory relationships
    quoted
  • low Secrets in code secret-high-entropy-token references/enrichr_guide.md:186
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `ENCO…015` - ENCODE histone ChIP-seq
    quoted
  • low Secrets in code secret-high-entropy-token references/enrichr_guide.md:202
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `COMP…025` - Experimental protein localization
    quoted
  • low Secrets in code secret-high-entropy-token SKILL_OLD.md:1068
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `Desc…021`
    quoted
  • low Secrets in code secret-high-entropy-token SKILL_OLD.md:1069
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `Alle…021`
    quoted
  • low Secrets in code secret-high-entropy-token SKILL_OLD.md:1077
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `ENCO…015`
    quoted
  • low Secrets in code secret-high-entropy-token SKILL_OLD.md:1083
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `COMP…025`, `COMP…025`
    quoted
  • low Secrets in code secret-high-entropy-token SKILL_OLD.md:1084
    High-entropy token-like string (may be an id, hash or a credential) (quoted — discussed, not commanded)
    - `DepM…023`
    quoted

Files scanned: 12. Evidence is masked. Grey chips explain why severity was lowered.

Against the Agent Skills spec

  • warning missing-ref reference to a missing file: ../tooluniverse-network-pharmacology/SKILL.md
  • warning missing-ref reference to a missing file: ../tooluniverse-multiomic-disease-characterization/SKILL.md
  • warning missing-ref reference to a missing file: ../tooluniverse-spatial-omics-analysis/SKILL.md
  • warning missing-ref reference to a missing file: ../tooluniverse-protein-interactions/SKILL.md

Process rating: all ten parameters 58/100

Will not run. References files that are not bundled: ../tooluniverse-network-pharmacology/SKILL.md, ../tooluniverse-multiomic-disease-characterization/SKILL.md, ../tooluniverse-spatial-omics-analysis/SKILL.md
  • 0Tools and files. 4 referenced file(s) missing: ../tooluniverse-network-pharmacology/SKILL.md, ../tooluniverse-multiomic-disease-characterization/SKILL.md, ../tooluniverse-spatial-omics-analysis/SKILL.md
  • 0Result and completion. Does not say what the result is
  • 0Progress reporting. Says nothing while it works
  • 30Running it twice. 3 mutating operations with no state check
  • 70Inputs and preconditions. Inputs and preconditions are listed
  • 85Steps. 46 steps, 1 vague phrases
  • 100When it triggers. States when to use and when not to
  • 100Failures and branches. 1 branches, has a failure section
  • 100Consistency. Name and required fields are in place
  • 100Execution cost. Instruction body is 3777 tokens
  • low 13 top-level sections: this looks like several domains in one skill

Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

Quality signals

  • +5Description has no quoted example phrases that should trigger the skill
  • +3Output format is not stated: the model decides each time
  • +1No license
  • +2Single-language instructions
  • +4Description says when NOT to use the skill
  • +3Description length 640: enough signal without eating the budget
  • +4Structure: 26 headings
  • +3Step-by-step instructions: 46 items
  • +4Has examples (12 code blocks)
  • +4Reference files are cited in the instructions (5 of 5)
  • +3All 1 scripts are documented

Quality base 70; lint remarks subtract, signals add up to 100. Result: 83.