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AC arboreto

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.

K-Dense-AI/claude-scientific-skills Agent Skills author: K-Dense-AI MIT 5 files · 1 script body ≈ 2 500 tokens Open the sourcegithub.com↗ analyzed 13 h ago

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.

As a process C 50/100 · Has gaps — weak spots: result and completion, when it triggers, inputs and preconditions

ProcedureGitHubSoftware developmentData and analyticsAI and agentstype 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
97/100
safety, quality, tests
Safety 60%
100
Quality 40%
92
Run on models
none yet
Process rating
C
50/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
When it triggers w 12
20
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: 5. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    • note edit-residue the text marks something as outdated (lines 32): check that old rules are not kept next to new ones — the full check reads the text for contradictions

    Process rating: all ten parameters 50/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 20When it triggers. No condition that starts the skill
    • 30Running it twice. 3 mutating operations with no state check
    • 50Failures and branches. 0 branches, has a failure section
    • 60Tools and files. Uses tools (web, python) that frontmatter does not declare
    • 100Steps. 10 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2500 tokens
    • 100Progress reporting. Reports progress
    • low 10 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
    • +4Description does not say when NOT to use the skill (false activations)
    • +3Output format is not stated: the model decides each time
    • +2Single-language instructions
    • +3Description length 268: enough signal without eating the budget
    • +4Structure: 11 headings
    • +3Step-by-step instructions: 10 items
    • +4Has examples (4 code blocks)
    • +4Reference files are cited in the instructions (3 of 3)
    • +3All 1 scripts are documented
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 92.