{"slug":"jaechang-hits-single-cell-annotation","name":"single-cell-annotation","description":"Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.","long_description":"---\nname: single-cell-annotation\ndescription: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.\nlicense: open\n---\n\n# Single Cell RNA-seq Cell Type Annotation\n\n---\n\n## Metadata\n\n**Short Description**: Best practices for annotating cell types in single-cell RNA-seq data using marker-based, automated, and reference-based approaches.\n\n**Authors**: Distilled from \"Single-cell best practices\" by Luecken, M.D. et al.\n\n**Affiliations**: Helmholtz Munich, Wellcome Sanger Institute, Harvard Medical School, and contributors\n\n**Version**: 1.0\n\n**Last Updated**: January 2025\n\n**License**: CC BY 4.0\n\n**Commercial Use**: ✅ Allowed\n\n**Source**: https://www.sc-best-practices.org/cellular_structure/annotation.html\n\n**Citation**: Luecken, M.D., Theis, F.J. et al. (2023). Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology.\n\n---\n\n## Overview\n\nCell type annotation is the process of assigning cell type labels to clusters or individual cells in single-cell RNA-seq data. This guide covers three main approaches and their practical implementation.\n\n## Key Concepts\n\n### Cell Type vs. Cell State\nA **cell type** is a stable identity defined by a developmental trajectory and core marker gene program (e.g., CD4+ T cell, hepatocyte). A **cell state** is a transient condition (activated, cycling, stressed) overlaid on a cell type. Annotation should target cell types first; states are attributes that may further subdivide a type but should not be conflated with type identity.\n\n### Marker Genes and Marker Panels\nMarker genes are genes whose expression is enriched in a specific cell type relative to other cells in the same tissue context. Reliable annotation uses **panels of multiple markers** (typically 3-5 per type) rather than a single gene, because expression is noisy in droplet-based scRNA-seq and many markers are shared across related types. Markers come in two flavors: **canonical** (literature-derived, e.g., CD3D for T cells) and **data-derived** (from differential expression on the dataset).\n\n### Reference Atlases and Label Transfer\nA reference atlas is a previously annotated dataset (e.g., Human Cell Atlas, Tabula Sapiens) used to project labels onto a new \"query\" dataset. Label transfer methods (scArches, scANVI, Azimuth, SingleR) align query cells into the reference latent space and assign the nearest neighbor's label. Quality of transfer depends on tissue match, technology match (e.g., 10x v3 vs. Smart-seq2), and species match.\n\n## Decision Framework\n\nUse this tree to choose an annotation approach:\n\n```\n                Do you have a well-characterized tissue\n                with a high-quality reference atlas?\n                            │\n              ┌─────────────┴─────────────┐\n              │                           │\n             YES                          NO\n              │                           │\n              ▼                           ▼\n   Is this a standard tissue       Are you studying\n   (PBMC, lung, gut) with a       novel cell types or\n   pre-trained classifier?         exploratory data?\n              │                           │\n        ┌─────┴─────┐               ┌─────┴─────┐\n        │           │               │           │\n       YES          NO             YES          NO\n        │           │               │           │\n        ▼           ▼               ▼           ▼\n   Automated    Reference-     Manual marker  Manual +\n   (CellTypist) based          based          automated\n                (scArches,     (Scanpy,       cross-check\n                 Azimuth,      Seurat)\n                 SingleR)\n```\n\n### Decision Table\n\n| Scenario | Approach | Primary Tool | Validation |\n|----------|----------|--------------|------------|\n| Standard human PBMC, large dataset (>100k cells) | Automated | CellTypist | Spot-check with manual markers |\n| Well-characterized tissue (lung, kidney, brain) | Reference-based label transfer | scArches / Azimuth | Marker consistency on top clusters |\n| Novel/rare tissue, no good reference | Manual marker-based | Scanpy / Seurat | Hierarchical, broad-to-fine |\n| Cross-species (e.g., zebrafish) | Manual markers + ortholog mapping | Scanpy + custom panel | Compare to closest reference species |\n| Developmental / continuous trajectory | Reference-based with state-aware model | scANVI / scArches | Trajectory coherence + markers |\n| Disease tissue with known perturbation | Manual + automated cross-check | CellTypist + Scanpy | Confirm disease-specific states separately |\n\n## Three Annotation Approaches\n\n### 1. Manual Marker-Based Annotation\nIdentify cell types by examining expression of known marker genes in each cluster.\n\n**Tools**: Scanpy, Seurat\n**Best for**: Small datasets, novel cell types, high confidence needs\n\n### 2. Automated Annotation\nUse pre-trained classifiers to automatically assign cell type labels.\n\n**Tools**: CellTypist, scAnnotate\n**Best for**: Standard tissues, quick preliminary annotation, large datasets\n\n### 3. Reference-Based Label Transfer\nTransfer labels from annotated reference datasets to your query data.\n\n**Tools**: scArches, scANVI, Azimuth, SingleR\n**Best for**: Well-characterized tissues, integration with public data\n\n## Recommended Workflow\n\n### Step 1: Quality Control First\n- **Remove low-quality cells before annotation**\n- Filter doublets (expected doublet rate: 0.8% per 1000 cells)\n- Check for ambient RNA contamination\n- Verify cluster quality and resolution\n\n### Step 2: Initial Marker-Based Assessment\n\n```python\n# Scanpy example\nimport scanpy as sc\n\n# Calculate marker genes for clusters\nsc.tl.rank_genes_groups(adata, 'leiden', method='wilcoxon')\n\n# Visualize top markers\nsc.pl.rank_genes_groups(adata, n_genes=25, sharey=False)\n\n# Plot known markers\nmarkers = {\n    'T cells': ['CD3D', 'CD3E', 'CD4', 'CD8A'],\n    'B cells': ['CD19', 'MS4A1', 'CD79A'],\n    'Monocytes': ['CD14', 'FCGR3A', 'LYZ'],\n    'NK cells': ['NCAM1', 'NKG7', 'GNLY']\n}\n\nsc.pl.dotplot(adata, markers, groupby='leiden')\n```\n\n### Step 3: Use Automated Tools for Validation\n\n```python\n# CellTypist example (fast, accurate for immune cells)\nimport celltypist\nfrom celltypist import models\n\n# Download immune cell model\nmodel = models.Model.load(model='Immune_All_Low.pkl')\n\n# Predict cell types\npredictions = celltypist.annotate(adata, model=model, majority_voting=True)\nadata = predictions.to_adata()\n```\n\n### Step 4: Reference-Based Refinement\n\n```python\n# scArches example for label transfer\nimport scarches as sca\n\n# Load pre-trained reference model\nmodel = sca.models.SCANVI.load_query_data(\n    adata=adata,  # Your query data\n    reference_model=\"path/to/reference_model\"\n)\n\n# Transfer labels\nmodel.train(max_epochs=100)\nadata.obs['transferred_labels'] = model.predict()\n```\n\n## Best Practices\n\n### Do's:\n1. **Always combine multiple approaches** - Use marker-based validation even with automated tools\n2. **Check cluster purity** - Ensure clusters represent single cell types\n3. **Validate with multiple marker sets** - Don't rely on single markers\n4. **Consider biological context** - Tissue type, disease state, developmental stage\n5. **Document confidence levels** - Note uncertain annotations\n6. **Use hierarchical annotation** - Broad categories first, then subtypes\n\n### Don'ts:\n1. **Don't over-cluster** - Too fine resolution creates artificial distinctions\n2. **Don't ignore batch effects** - Correct before annotation\n3. **Don't trust automation blindly** - Always validate predictions\n4. **Don't mix cell states with cell types** - Activated vs. resting cells are states, not types\n5. **Don't annotate low-quality cells** - Remove them first\n\n## Common Pitfalls\n\n1. **Doublet Clusters**: Clusters that show markers from multiple cell types are often doublets, not novel hybrid populations.\n   - *How to avoid*: Run doublet detection tools (Scrublet, DoubletFinder) before annotation and remove flagged cells.\n2. **Ambient RNA Contamination**: Background markers appear across all cells, blurring cell type boundaries.\n   - *How to avoid*: Apply SoupX or CellBender decontamination during preprocessing — don't trust raw counts on droplet data.\n3. **Over-interpretation of Small Clusters**: Rare clusters (<25 cells) are often technical artifacts rather than biological subtypes.\n   - *How to avoid*: Require a minimum cell count threshold and validate with an independent dataset before naming the cluster.\n4. **Reference Mismatch**: Transferring labels from a reference built on a different tissue, species, or condition produces confidently wrong annotations.\n   - *How to avoid*: Use tissue- and species-matched references, and check marker-gene overlap between query and reference before label transfer.\n5. **Confusing Cell States with Cell Types**: Activated vs. resting T cells, M1 vs. M2 macrophages, and cycling vs. quiescent cells are *states*, not distinct types.\n   - *How to avoid*: Annotate cell type first using stable lineage markers, then layer state annotations on top — don't mix the two axes.\n6. **Trusting Automated Tools Blindly**: CellTypist or SingleR predictions look authoritative but can fail silently on out-of-distribution cells.\n   - *How to avoid*: Always cross-check automated calls against marker-based dot plots, and flag low-confidence predictions for manual review.\n7. **Annotating Low-Quality Cells**: Including cells with high mitochondrial content or low gene counts contaminates downstream signatures.\n   - *How to avoid*: Apply QC filters (mt%, n_genes, n_counts) before clustering — don't annotate first and clean up later.\n\n## Tool Selection Guide\n\n| Scenario | Recommended Tool | Why |\n|----------|------------------|-----|\n| Immune cells (human) | CellTypist | Pre-trained on large immune atlases |\n| Mouse tissues | scArches + Mouse Cell Atlas | Comprehensive mouse reference |\n| Novel cell types | Manual + Scanpy/Seurat | Need domain expertise |\n| Large datasets (>100k cells) | CellTypist | Fast, scalable |\n| Cross-species | Manual markers | Limited reference transfer |\n| Developmental data | scArches | Handles continuous states |\n\n## Key Marker Genes by Cell Type\n\n### Blood/Immune:\n- **T cells**: CD3D, CD3E (all T cells); CD4, CD8A (subtypes)\n- **B cells**: CD19, MS4A1 (CD20), CD79A\n- **Monocytes/Macrophages**: CD14, CD68, LYZ\n- **NK cells**: NCAM1 (CD56), NKG7, KLRD1\n- **Dendritic cells**: FCER1A, CD1C\n\n### Epithelial:\n- **General epithelial**: EPCAM, KRT18, KRT19\n- **Lung AT1**: AGER, PDPN\n- **Lung AT2**: SFTPC, SFTPA1\n- **Intestinal**: VIL1, MUC2\n\n### Stromal:\n- **Fibroblasts**: COL1A1, DCN, LUM\n- **Endothelial**: PECAM1 (CD31), VWF, CDH5\n- **Smooth muscle**: ACTA2, MYH11, TAGLN\n\n## Validation Checklist\n\n- [ ] Cluster purity: >80% cells with same label per cluster\n- [ ] Marker consistency: Top DE genes match expected markers\n- [ ] Biological plausibility: Expected proportions for tissue type\n- [ ] Cross-method agreement: Manual and automated annotations align\n- [ ] Reference quality: >70% cells successfully transferred\n- [ ] Doublet check: No clusters with multi-lineage markers\n- [ ] Documentation: Record confidence levels and uncertain calls\n\n## References\n\n### Tools:\n- **Scanpy**: https://scanpy.readthedocs.io/\n- **CellTypist**: https://www.celltypist.org/\n- **scArches**: https://scarches.readthedocs.io/\n- **Seurat**: https://satijalab.org/seurat/\n\n### Marker Databases & Atlases:\n- **PanglaoDB**: https://panglaodb.se/ (Database of marker genes)\n- **CellMarker**: http://bio-bigdata.hrbmu.edu.cn/CellMarker/ (Curated cell marker database)\n- **Human Cell Atlas**: https://www.humancellatlas.org/ (Reference datasets)\n- **Single Cell Best Practices**: https://www.sc-best-practices.org/cellular_structure/annotation.html\n- **Luecken & Theis (2023)**: Current best practices in single-cell RNA-seq analysis. Molecular Systems Biology.\n\n### Pre-trained Models:\n- **CellTypist models**: 30+ tissue-specific models\n- **Azimuth references*","tagline":"Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.","category":"automation","tags":["agent-skill"],"author":"jaechang-hits","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github fast track","sourceDetail":"jaechang-hits/SciAgent-Skills","creatorName":"jaechang-hits","creatorUrl":"https://github.com/jaechang-hits","sourceUrl":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation#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. 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issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["automation","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","trust_score":70,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["automation","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":78,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"trust_score_v4":{"version":"trust-score-v4","score":78,"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":62,"weight":0.13,"status":"info","detail":"359 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"8d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"open"},{"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":74,"weight":0.12,"status":"info","detail":"network or browser surface, database surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation"},{"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":60,"weight":0.07,"status":"warn","detail":"filesystem or document access, network or browser access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation"},{"id":"review_status","label":"Review status","score":88,"weight":0.05,"status":"pass","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":"info","label":"GitHub adoption","detail":"359 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"359 stars, 35 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"8d since push"},{"status":"pass","label":"License clarity","detail":"open"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"info","label":"Dependency/runtime risk","detail":"network or browser surface, database surface"},{"status":"pass","label":"Install availability","detail":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"filesystem or document access, network or browser access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation"},{"status":"pass","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","Install command has no obvious high-risk pattern"],"warnings":["Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"],"evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"8d since push","license":"open","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","install":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","installSafety":"standard package or runtime install path","permissionSurface":"filesystem or document access, network or browser access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","8d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; 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issue activity unavailable in current metadata","Permission surface: filesystem or document access, 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"]},"outcome_stats":null,"safety":{"score":62,"level":"review_before_install","label":"Review before install","safety_tier":{"tier":"reviewed","label":"Reviewed with permission notes","badge":"REVIEWED","summary":"Usable candidate, but the agent should surface permission and audit notes before installation.","recommended_action":"Require human approval before installing into a real workspace.","auto_install_policy":"review","reasons":["Permission surface may require sandboxing","62/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"database","label":"Database access","reason":"Skill may inspect schemas, query databases, or work with persistent stores.","severity":"medium"}],"policy_warnings":["Permission surface may require sandboxing"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","badge":"REVIEWED","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Require human approval before installing into a real workspace.","reasons":["Permission surface may require sandboxing","62/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"review","score":76,"risk_level":"medium","decision":{"recommendation":"manual_review","reason":"Require human approval before installing into a real workspace.","auto_install_allowed":false,"policy":"review","human_review_required":true},"blockers":[],"warnings":["Trust score: Good trust signals with a few areas worth checking before rollout.","Audit score: Needs review","Agent safety gate: Usable candidate, but the agent should surface permission and audit notes before installation.","Permission surface: filesystem or document access, network or browser access","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":94,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate single-cell-annotation before installing it in an agent workflow","automation","Browser automation workflows; Claude Code teams; builders willing to evaluate younger projects"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation"]},{"id":"trust_score","label":"Trust score","status":"warn","score":78,"required_for_auto_install":true,"detail":"Good trust signals with a few areas worth checking before rollout.","evidence":["Strong shortlist","359 GitHub stars","open"]},{"id":"audit_score","label":"Audit score","status":"warn","score":82,"required_for_auto_install":true,"detail":"Needs review","evidence":["Permission surface may require sandboxing"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":62,"required_for_auto_install":true,"detail":"Usable candidate, but the agent should surface permission and audit notes before installation.","evidence":["Require human approval before installing into a real workspace.","Permission surface may require sandboxing"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"open","evidence":["open"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"8d since push","evidence":["8d since push"]},{"id":"permission_surface","label":"Permission surface","status":"warn","score":60,"required_for_auto_install":true,"detail":"filesystem or document access, network or browser access","evidence":["Network access: medium","Filesystem access: medium","Database access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation/evals","api":"/api/agent/evals?slug=jaechang-hits-single-cell-annotation","text":"/api/agent/evals?slug=jaechang-hits-single-cell-annotation&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"jaechang-hits-single-cell-annotation","name":"single-cell-annotation","description":"Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.","category":"automation","url":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","github_repo":"jaechang-hits/SciAgent-Skills"},"suited_tasks":["Browser automation workflows","Claude Code teams","builders willing to evaluate younger projects","Navigate pages","Click and type safely","Check visual and DOM state","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","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 jaechang-hits-single-cell-annotation"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"single-cell-annotation\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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/jaechang-hits-single-cell-annotation/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-single-cell-annotation"},"trust":{"score":78,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"8d since push","license":"open","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","install":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","installSafety":"standard package or runtime install path","permissionSurface":"filesystem or document access, 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":["automation","agent-skill"],"known_risks":["Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, 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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"]},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Require human approval before installing into a real workspace."},"quality":{"score":72,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"8d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"],"agent_contract":{"task_input":"Use single-cell-annotation in an agent workflow","recommended_action":"Require human approval before installing into a real workspace.","install_policy":"review","minimum_review_before_use":["Trust: 78/100 Strong shortlist","Audit: 82/100 Needs review","Safety: 62/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"jaechang-hits-single-cell-annotation (single-cell-annotation)","install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","risk_summary":"Needs review; Reviewed with permission notes; 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":"jaechang-hits-single-cell-annotation","task":"Use single-cell-annotation 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/jaechang-hits-single-cell-annotation","api":"https://www.openagentskill.com/api/agent/skills/jaechang-hits-single-cell-annotation","audit":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=jaechang-hits-single-cell-annotation&task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/jaechang-hits-single-cell-annotation/install","manifest":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-single-cell-annotation"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"jaechang-hits-single-cell-annotation","name":"single-cell-annotation","description":"Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.","category":"automation","url":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","github_repo":"jaechang-hits/SciAgent-Skills"},"suited_tasks":["Browser automation workflows","Claude Code teams","builders willing to evaluate younger projects","Navigate pages","Click and type safely","Check visual and DOM state","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","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 jaechang-hits-single-cell-annotation"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"single-cell-annotation\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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/jaechang-hits-single-cell-annotation/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-single-cell-annotation"},"trust":{"score":78,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"359 GitHub stars","repoActivity":"359 stars, 35 forks","lastPushed":"8d since push","license":"open","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","install":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","installSafety":"standard package or runtime install path","permissionSurface":"filesystem or document access, 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":["automation","agent-skill"],"known_risks":["Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, 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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"]},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Require human approval before installing into a real workspace."},"quality":{"score":72,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"8d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"],"agent_contract":{"task_input":"Use single-cell-annotation in an agent workflow","recommended_action":"Require human approval before installing into a real workspace.","install_policy":"review","minimum_review_before_use":["Trust: 78/100 Strong shortlist","Audit: 82/100 Needs review","Safety: 62/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"jaechang-hits-single-cell-annotation (single-cell-annotation)","install_command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","risk_summary":"Needs review; Reviewed with permission notes; 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":"jaechang-hits-single-cell-annotation","task":"Use single-cell-annotation 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/jaechang-hits-single-cell-annotation","api":"https://www.openagentskill.com/api/agent/skills/jaechang-hits-single-cell-annotation","audit":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=jaechang-hits-single-cell-annotation&task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20single-cell-annotation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/jaechang-hits-single-cell-annotation/install","manifest":"https://www.openagentskill.com/api/registry/manifest/jaechang-hits-single-cell-annotation"}},"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":"browser-automation","title":"Browser automation"},{"slug":"research-agents","title":"Research agents"},{"slug":"workflow-automation","title":"Workflow automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":359,"starsLabel":"359","forks":35,"license":"open","qualityScore":72,"trustScore":78,"auditScore":82},"maintenance":{"status":"fresh","label":"8d since push","daysSincePush":8,"lastPushedAt":"2026-08-29T00:42:20+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"]},"coverageTags":["Research","Research agents","automation","agent-skill"]},"audit":{"audit_score":82,"risk_level":"needs_review","risk_label":"Needs review","quality_score":72,"trust_score":78,"maintenance_score":100,"security_score":83,"install_score":92,"warnings":["Permission surface may require sandboxing","Quality score needs review","Permission surface needs review: filesystem or document access, network or browser access","Stars/forks activity: 359 stars, 35 forks; issue activity unavailable in current metadata","Permission surface: filesystem or document access, network or browser access"]},"quality_signals":{"model":"v2","star_score":17.89,"usage_score":0,"review_score":5.1,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"}],"stacks":[{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"},{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"}],"install":"npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation","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 jaechang-hits-single-cell-annotation","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 \"single-cell-annotation\" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" as a Claude Code skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation. 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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 \"single-cell-annotation\" from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation 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: Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. 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\":\"jaechang-hits-single-cell-annotation\",\"task\":\"Install single-cell-annotation\",\"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/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","github_repo":"jaechang-hits/SciAgent-Skills","version":"1.0.0","license":"open","urls":{"web":"https://www.openagentskill.com/skills/jaechang-hits-single-cell-annotation","repository":"https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation","api":"/api/agent/skills/jaechang-hits-single-cell-annotation","install_api":"/api/skills/jaechang-hits-single-cell-annotation/install"},"meta":{"created_at":"2026-09-03T11:33:05.37737+00:00","updated_at":"2026-09-03T11:33:05.440212+00:00","agent_friendly":true}}