scvi-tools

Run scvi-tools single-cell workflows. Use when a task asks for scVI/scANVI setup, latent embeddings, batch correction, differential expression, cell annotation, or reproducible AnnData analysis.

Quality

76%

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Quality

Content

75%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A concise, well-sequenced workflow that assumes domain competence and includes pre-training verification and post-training QC checkpoints. Its main weakness is actionability: it tells Claude what to record and check but not how to execute or verify via concrete commands or code.

Suggestions

Add concrete executable examples or commands for the key actions (e.g. a minimal scVI/scANVI training snippet or a verification command) to lift actionability.

Add an explicit feedback loop after step 4 (e.g. 'If batch mixing is poor or markers are inconsistent, adjust hyperparameters/covariates and retrain') to make the validation checkpoint a true retry loop.

Introduce light subheadings (e.g. '## Inputs to record', '## Verification', '## QC checks') to improve navigation of the flat workflow list.

Dimension	Reasoning	Score
Conciseness	The body is lean with no concept over-explanation, assuming Claude's knowledge of scvi-tools; each line (record fields, verify environment, save artifacts, check metrics) earns its place.	5 / 5
Actionability	Steps list specific items to capture and check (batch keys, label keys, marker consistency) but provide no executable code or commands; guidance is concrete in content yet incomplete in execution detail.	3 / 5
Workflow Clarity	A clear five-step numbered sequence includes verification checkpoints (step 2 'Verify ... before training', step 4 'Check ...'), satisfying the batch-operation validation requirement, though an explicit feedback loop ('if metrics fail, retrain') is not stated.	4 / 5
Progressive Disclosure	As a short single-file skill with no bundle files, content is reasonably organized under a 'Workflow' heading with a closing guardrail note; structure is good but flat, with minor organization gaps rather than the clean sectioned overview of a 5.	4 / 5
	Total	16 / 20 Passed

Description

78%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, domain-specific description that clearly states purpose and explicit trigger conditions using natural single-cell biology vocabulary. It is concise and low-conflict, with only minor room to broaden trigger synonyms and sharpen the 'what' phrasing.

Suggestions

Add common synonyms users may say, e.g. 'scRNA-seq' or 'single-cell RNA-seq', to the trigger clause for broader keyword coverage.

Tighten the 'what' clause beyond 'Run scvi-tools single-cell workflows' to a more concrete action list mirroring the trigger terms.

Dimension	Reasoning	Score
Specificity	The description names several concrete capabilities ('scVI/scANVI setup, latent embeddings, batch correction, differential expression, cell annotation ... AnnData analysis'), giving broad coverage of the domain, though the lead 'Run scvi-tools single-cell workflows' is a somewhat umbrella action statement.	4 / 5
Completeness	Both 'what' ('Run scvi-tools single-cell workflows') and an explicit 'when' ('Use when a task asks for ...') with concrete trigger phrases are present; the 'what' could be slightly more specific than the umbrella workflow phrasing.	4 / 5
Trigger Term Quality	Natural single-cell terms a practitioner would actually say (scVI, scANVI, latent embeddings, batch correction, differential expression, cell annotation, AnnData) are present, but a few common variants (e.g. 'single-cell RNA-seq', 'scRNA-seq') are missing.	4 / 5
Distinctiveness Conflict Risk	scvi-tools with scVI/scANVI/AnnData triggers occupies a clear single-cell niche with distinctive terminology, giving minimal overlap risk with unrelated skills.	5 / 5
	Total	17 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: companion-inc/feynman
Path: skills/scvi-tools/SKILL.md
Commit: 95c51d9

Reviewed: about 8 hours ago

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