{"slug":"k-dense-ai-cellxgene-census","name":"cellxgene-census","description":"Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.","tagline":"Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or refer","category":"research","tags":["agent-skill"],"author":{"name":"K-Dense-AI","verified":false,"url":"https://github.com/K-Dense-AI"},"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"K-Dense-AI/scientific-agent-skills","creatorName":"K-Dense-AI","creatorUrl":"https://github.com/K-Dense-AI","sourceUrl":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":38487,"forks":3607,"verified_installs":0,"install_attempts":0,"successful_runs":0,"total_outcomes":0,"downloads":0,"rating":0,"review_count":0,"quality_score":55.05},"quality":{"score":92,"tier":"excellent","label":"Excellent","summary":"High-confidence pick with strong adoption and healthy maintenance signals.","signals":[{"label":"GitHub stars","value":"38K","tone":"positive"},{"label":"Freshness","value":"6d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT","tone":"neutral"}],"warnings":["The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary."]},"trust":{"version":"trust-score-v4","score":73,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout.","recommendedAction":"Test in a sandbox workflow and compare its install path with close alternatives.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"38K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"6d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, external package install surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":50,"weight":0.07,"status":"warn","detail":"shell or command execution, network or browser access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"pass","label":"GitHub adoption","detail":"38K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"6d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, external package install surface"},{"status":"pass","label":"Install availability","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, network or browser access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Large GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; 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this broadens the agent attack surface more than necessary.","Permission surface needs review: shell or command execution, network or browser access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, network or browser access"]},"safety":{"score":56,"level":"review_before_install","label":"Review before install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["High-risk permission hints: Shell or command execution","56/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"database","label":"Database access","reason":"Skill may inspect schemas, query databases, or work with persistent stores.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["High-risk permission hints: Shell or command execution","56/100 agent safety score"]},"supply_profile":{"track":{"slug":"research","label":"Research and knowledge work","shortLabel":"Research","description":"Deep research, source comparison, literature review, RAG, knowledge search, and reports."},"scenario":{"label":"Research agents","description":"I need my agent to research a topic, compare sources, and produce a concise report.","useCases":[{"slug":"research-agents","title":"Research agents"},{"slug":"rag-knowledge","title":"RAG and knowledge"},{"slug":"github-automation","title":"GitHub automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":38487,"starsLabel":"38K","forks":3607,"license":"MIT","qualityScore":92,"trustScore":73,"auditScore":84},"maintenance":{"status":"fresh","label":"6d since push","daysSincePush":6,"lastPushedAt":"2026-08-30T13:19:27+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; 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references are present and appear substantive."]},"decision":{"readiness_score":100,"readiness_label":"Production-ready","headline":"Primary pick for Research agents","role":"Primary pick","primary_fit":"Research agents","best_for":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals"],"risks":["The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","No OpenAgentSkill engagement data yet"],"next_steps":["Install it in a sandbox agent and run one Research agents task end to end.","Compare output quality, latency, and failure behavior against at least one alternative.","Promote it into production only after reviewing repository permissions, license, and maintenance signals."]},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-cellxgene-census","name":"cellxgene-census","description":"Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.","category":"research","url":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Chunk documents","Create embeddings"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-cellxgene-census"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"cellxgene-census\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"cellxgene-census\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"cellxgene-census\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/k-dense-ai-cellxgene-census/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-cellxgene-census"},"trust":{"score":73,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"MIT","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, network or browser access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["research","agent-skill"],"known_risks":["The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","Permission surface needs review: shell or command execution, network or browser access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, network or browser access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":84,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","The SKILL.md excerpt does not include an explicit safe-handling note that values from public datasets should be treated as untrusted data, especially when used in dynamically constructed filters or displayed to users.","The excerpt is truncated, so completeness of setup, limitations, and error-handling documentation could not be fully verified from SKILL.md alone; references are present and appear substantive.","Permission surface needs review: shell or command execution, network or browser access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, network or browser access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","The SKILL.md excerpt does not include an explicit safe-handling note that values from public datasets should be treated as untrusted data, especially when used in dynamically constructed filters or displayed to users."],"agent_contract":{"task_input":"Use cellxgene-census in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 73/100 Strong shortlist","Audit: 84/100 Needs review","Safety: 56/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-cellxgene-census (cellxgene-census)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"k-dense-ai-cellxgene-census","task":"Use cellxgene-census in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-cellxgene-census","audit":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-cellxgene-census&task=Use%20cellxgene-census%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20cellxgene-census%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20cellxgene-census%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-cellxgene-census/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-cellxgene-census"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-cellxgene-census","name":"cellxgene-census","description":"Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.","category":"research","url":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Chunk documents","Create embeddings"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-cellxgene-census"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"cellxgene-census\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"cellxgene-census\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"cellxgene-census\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/k-dense-ai-cellxgene-census/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-cellxgene-census"},"trust":{"score":73,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"MIT","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, network or browser access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["research","agent-skill"],"known_risks":["The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","Permission surface needs review: shell or command execution, network or browser access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, network or browser access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":84,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","The SKILL.md excerpt does not include an explicit safe-handling note that values from public datasets should be treated as untrusted data, especially when used in dynamically constructed filters or displayed to users.","The excerpt is truncated, so completeness of setup, limitations, and error-handling documentation could not be fully verified from SKILL.md alone; references are present and appear substantive.","Permission surface needs review: shell or command execution, network or browser access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, network or browser access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The skill declares Bash, Write, and Edit permissions even though the core workflow is read-only querying of public Census data; this broadens the agent attack surface more than necessary.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","The SKILL.md excerpt does not include an explicit safe-handling note that values from public datasets should be treated as untrusted data, especially when used in dynamically constructed filters or displayed to users."],"agent_contract":{"task_input":"Use cellxgene-census in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 73/100 Strong shortlist","Audit: 84/100 Needs review","Safety: 56/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-cellxgene-census (cellxgene-census)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"k-dense-ai-cellxgene-census","task":"Use cellxgene-census in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-cellxgene-census","audit":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-cellxgene-census&task=Use%20cellxgene-census%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20cellxgene-census%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20cellxgene-census%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-cellxgene-census/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-cellxgene-census"}},"platforms":["Claude Code"],"use_cases":[{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"}],"install":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-cellxgene-census","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"cellxgene-census\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"cellxgene-census\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"cellxgene-census\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-cellxgene-census\",\"task\":\"Install cellxgene-census\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census","github_repo":"K-Dense-AI/scientific-agent-skills","version":"1.0.0","license":"MIT","updated_at":"2026-09-01T11:59:28.941454+00:00","canonical_key":"k-dense-ai/scientific-agent-skills#skills/cellxgene-census","recommendation_reasons":["Strong GitHub adoption: 38,487 stars","Install handoff is available","Repository freshness signal is available"],"urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-cellxgene-census","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-cellxgene-census/install","audit":"https://www.openagentskill.com/skills/k-dense-ai-cellxgene-census/audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/cellxgene-census"},"meta":{"endpoint":"/api/registry/manifest/{slug}","canonical_agent_endpoint":"/api/agent/skills/k-dense-ai-cellxgene-census","agent_friendly":true,"api_version":"1.0","generated_at":"2026-09-06T08:11:48.626Z"}}