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AC pathway-enrichment

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".

K-Dense-AI/claude-scientific-skills Agent Skills author: K-Dense-AI MIT 6 files · 1 script body ≈ 3 817 tokens Open the sourcegithub.com↗ analyzed 13 h ago

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.

As a process C 58/100 · Has gaps — weak spots: result and completion, inputs and preconditions, running it twice

AnalyzerData and analyticstype 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
A
98/100
safety, quality, tests
Safety 60%
100
Quality 40%
94
Run on models
none yet
Process rating
C
58/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Running it twice w 4
30
the three weakest of ten parameters · all ten

How to improve

    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 · 0

    ✓ No critical or high findings

    Files scanned: 6. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    ✓ No remarks against the Agent Skills spec

    Process rating: all ten parameters 58/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 30Running it twice. 3 mutating operations with no state check
    • 50Failures and branches. 0 branches, has a failure section
    • 60Tools and files. Uses tools (bash, web, python) that frontmatter does not declare
    • 85Steps. 27 steps, 1 vague phrases
    • 100When it triggers. States when to use and when not to
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 3817 tokens
    • 100Progress reporting. Reports progress
    • low 12 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

    • +4Description does not say when NOT to use the skill (false activations)
    • +3Description length 1011: 120–800 characters recommended
    • +3Output format is not stated: the model decides each time
    • +2Single-language instructions
    • +5Description quotes 7 example trigger phrases
    • +4Structure: 23 headings
    • +3Step-by-step instructions: 27 items
    • +4Has examples (5 code blocks)
    • +4Reference files are cited in the instructions (4 of 4)
    • +3All 1 scripts are documented
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 94.

    In the sandbox Скрипты не запустились

    The skill's scripts were run in a throwaway machine: no network, fake keys in the home directory, a tracer watching. We wrote down what they did. Reaching for the network or for secrets caps the technical grade at C; a quiet run adds no points.

    Запущено 1 скрипт; каждому дали двадцать секунд, поддельный домашний каталог с ключами и сеть, в которой ничего нет.

    Ни один не дошёл до работы — им не хватило зависимостей, аргументов или файлов. Это не отзыв о поведении: наблюдать было не за чем.

    scripts/run_enrichment.pyне запустился: ModuleNotFoundError: No module named 'numpy'

    5 Oct 2026