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scvi-tools

Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.

70

Quality

87%

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SKILL.md
Quality
Evals
Security

Quality

Content

82%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.

An action-dense, executable skill body with clear sequencing and validation for a destructive/batch GPU workflow. Conciseness and progressive-disclosure are strong but not maximal due to minor trims possible and the absence of separate reference files.

DimensionReasoningScore

Conciseness

Lean and assumes Claude's competence — no padding about what scRNA-seq or libraries are — with tight code blocks and compact gotcha/troubleshooting tables; a few explanatory sentences could be trimmed, placing it just below the fully-lean anchor-5.

4 / 5

Actionability

Copy-paste-ready scVI/scANVI/DE code blocks with real kwargs, a runnable Modal pipeline.py, and the explicit exec(open(...kernel.py)) loader covering the common cases, matching the anchor-5 executable example.

5 / 5

Workflow Clarity

Clear setup→scVI→scANVI→DE→output→remote sequence with validation (h5ad_safe_obs before write) and an error-recovery troubleshooting table; not a strict numbered validate→fix→retry checklist so it sits below anchor-5.

4 / 5

Progressive Disclosure

Well-organized into clearly-labeled sections (Setup, How to run, DE, Output, Remote compute, Gotchas, Troubleshooting) with easy internal navigation; no bundle files exist to provide one-level-deep references, so it cannot reach the anchor-5 external-split example.

4 / 5

Total

17

/

20

Passed

Description

92%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 specific, well-triggered description that clearly states capabilities, when to reach for the skill, and where not to use it. Minor trigger-term synonym coverage (e.g. h5ad/UMI) keeps it just off perfect.

DimensionReasoningScore

Specificity

Names the domain and multiple concrete actions — 'integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster' — plus the specific methods (scVI/scANVI/DE), giving comprehensive coverage matching the anchor-5 example.

5 / 5

Completeness

Explicitly answers both what (scVI/scANVI/DE capabilities) and when via the concrete 'Reach for this skill to integrate... embed... transfer... score...' trigger clause, matching the anchor-5 example.

5 / 5

Trigger Term Quality

Strong natural-phrase coverage ('integrate scRNA-seq batches', 'embed cells for clustering', 'label transfer', 'differentially expressed genes'), but missing common synonyms a user might say like 'h5ad' or 'UMI counts', so it sits just below the comprehensive anchor-5 example.

4 / 5

Distinctiveness Conflict Risk

Clear niche (scvi-tools scRNA-seq integration) with explicit boundary guidance steering spatial deconvolution to 'cell2location, DestVI, or Tangram methods instead', minimizing conflict with sibling skills.

5 / 5

Total

19

/

20

Passed

Validation

87%

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

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

14

/

16

Passed

Repository
UnicomAI/wanwu
Reviewed

Table of Contents

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