SKILLEMALL.ai
GitHub ↗ RU Sign in

AC scgpt

Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.

aipoch/open-science Agent Skills author: aipoch Apache-2.0 1 file body ≈ 1 231 tokens Open the sourcegithub.com↗ analyzed 2 d ago

Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.

As a process C 61/100 · Has gaps — weak spots: when it triggers, running it twice, progress reporting

IntegrationAI 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
95/100
safety, quality, tests
Safety 60%
100
Quality 40%
87
Run on models
none yet
Process rating
C
61/100
Has gaps
Progress reporting w 2
0
When it triggers w 12
20
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: 1. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    • note frontmatter-key unknown frontmatter key "requirements"

    Process rating: all ten parameters 61/100

    • 0Progress reporting. Says nothing while it works
    • 20When it triggers. No condition that starts the skill
    • 30Running it twice. 4 mutating operations with no state check
    • 50Failures and branches. 0 branches, has a failure section
    • 60Tools and files. Uses tools (python) that frontmatter does not declare
    • 60Result and completion. Output format stated, no completion criterion
    • 70Inputs and preconditions. Inputs and preconditions are listed
    • 75Steps. 3 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 1231 tokens

    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)
    • +2Single-language instructions
    • +3Description length 383: enough signal without eating the budget
    • +4Structure: 9 headings
    • +3Step-by-step instructions: 3 items
    • +3Output format is stated explicitly
    • +4Has examples (3 code blocks)
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 87.