{"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.","long_description":"---\nname: cellxgene-census\ndescription: 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.\nallowed-tools: Read Write Edit Bash\nlicense: MIT\ncompatibility: Requires Python >=3.10,<3.13. Examples target cellxgene-census 1.17.x and the 2025-11-08 stable LTS Census; spatial workflows need the spatial extra and TileDB-SOMA >=1.15.5. No authentication is required for public Census data.\nmetadata:\n  version: \"1.2\"\n  skill-author: K-Dense Inc.\n---\n\n# CZ CELLxGENE Census\n\n## Overview\n\nThe CZ CELLxGENE Census provides programmatic access to a comprehensive, versioned collection of standardized single-cell and spatial transcriptomics data from CZ CELLxGENE Discover. This skill enables efficient querying and analysis of public Census releases without downloading whole datasets first.\n\nThe Census includes:\n- **217+ million total cells** and **125+ million unique cells** in the 2025-11-08 stable LTS release\n- **1,845 datasets** in the 2025-11-08 stable LTS release\n- **Human, mouse, marmoset, rhesus macaque, and chimpanzee** data in the current schema\n- **Standardized metadata** (cell types, tissues, diseases, donors)\n- **Raw gene expression** matrices and source H5AD lookup/download helpers\n- **Pre-calculated summary counts, embeddings, and spatial data**\n- **Integration with AnnData, Scanpy, TileDB-SOMA, TileDB-SOMA-ML, and other analysis tools**\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Querying single-cell expression data by cell type, tissue, or disease\n- Exploring available single-cell datasets and metadata\n- Training machine learning models on single-cell data\n- Performing large-scale cross-dataset analyses\n- Integrating Census data with scanpy or other analysis frameworks\n- Computing statistics across millions of cells\n- Accessing pre-calculated embeddings or model predictions\n\n## Installation and Setup\n\nInstall the Census API:\n```bash\nuv pip install \"cellxgene-census==1.17.*\"\n```\n\nFor spatial workflows:\n```bash\nuv pip install \"cellxgene-census[spatial]==1.17.*\" \"spatialdata[extra]>=0.2.5\"\n```\n\nFor PyTorch model training, use TileDB-SOMA-ML. The old `cellxgene_census.experimental.ml` loaders are deprecated:\n\n```bash\nuv pip install \"cellxgene-census==1.17.*\" tiledbsoma-ml\n```\n\n## Core Workflow Patterns\n\nEight patterns, each with code, are in\n[references/core_workflow_patterns.md](references/core_workflow_patterns.md):\n\n1. **Opening the Census** — always pin `census_version` so an analysis stays reproducible.\n2. **Exploring Census information** — available datasets, cell counts, and summary tables.\n3. **Querying expression data** — small to medium scale into an `AnnData`.\n4. **Large-scale queries** — out-of-core processing when the slice will not fit in memory.\n5. **Machine learning with PyTorch** — the Census data loaders.\n6. **Spatial Census data** — accessing spatial assays.\n7. **Integration with Scanpy** — handing a Census slice to a standard Scanpy workflow.\n8. **Multi-dataset integration** — combining datasets and handling batch effects.\n\n## Key Concepts and Best Practices\n\n### Always Filter for Primary Data\nUnless analyzing duplicates, always include `is_primary_data == True` in queries to avoid counting cells multiple times:\n```python\nobs_value_filter=\"cell_type == 'B cell' and is_primary_data == True\"\n```\n\n### Specify Census Version for Reproducibility\nAlways specify the Census version in production analyses:\n```python\ncensus = cellxgene_census.open_soma(census_version=\"2025-11-08\")\n```\n\n### Estimate Query Size Before Loading\nFor large queries, first check the number of cells to avoid memory issues:\n```python\n# Get cell count\nmetadata = cellxgene_census.get_obs(\n    census, \"homo_sapiens\",\n    value_filter=\"tissue_general == 'brain' and is_primary_data == True\",\n    column_names=[\"soma_joinid\"]\n)\nn_cells = len(metadata)\nprint(f\"Query will return {n_cells:,} cells\")\n\n# If too large (>100k), use out-of-core processing\n```\n\n### Use tissue_general for Broader Groupings\nThe `tissue_general` field provides coarser categories than `tissue`, useful for cross-tissue analyses:\n```python\n# Broader grouping\nobs_value_filter=\"tissue_general == 'immune system'\"\n\n# Specific tissue\nobs_value_filter=\"tissue == 'peripheral blood mononuclear cell'\"\n```\n\n### Select Only Needed Columns\nMinimize data transfer by specifying only required metadata columns:\n```python\nobs_column_names=[\"cell_type\", \"tissue_general\", \"disease\"]  # Not all columns\n```\n\n### Check Dataset Presence for Gene-Specific Queries\nWhen analyzing specific genes, verify which datasets measured them:\n```python\npresence = cellxgene_census.get_presence_matrix(\n    census,\n    \"homo_sapiens\",\n    var_value_filter=\"feature_name in ['CD4', 'CD8A']\"\n)\n```\n\n### Two-Step Workflow: Explore Then Query\nFirst explore metadata to understand available data, then query expression:\n```python\n# Step 1: Explore what's available\nmetadata = cellxgene_census.get_obs(\n    census, \"homo_sapiens\",\n    value_filter=\"disease == 'COVID-19' and is_primary_data == True\",\n    column_names=[\"cell_type\", \"tissue_general\"]\n)\nprint(metadata.value_counts())\n\n# Step 2: Query based on findings\nadata = cellxgene_census.get_anndata(\n    census=census,\n    organism=\"Homo sapiens\",\n    obs_value_filter=\"disease == 'COVID-19' and cell_type == 'T cell' and is_primary_data == True\",\n)\n```\n\n## Available Metadata Fields\n\n### Cell Metadata (obs)\nKey fields for filtering:\n- `cell_type`, `cell_type_ontology_term_id`\n- `tissue`, `tissue_general`, `tissue_ontology_term_id`\n- `disease`, `disease_ontology_term_id`\n- `assay`, `assay_ontology_term_id`\n- `donor_id`, `sex`, `self_reported_ethnicity`\n- `development_stage`, `development_stage_ontology_term_id`\n- `dataset_id`\n- `is_primary_data` (Boolean: True = unique cell)\n\nThe current schema includes organism collections beyond human and mouse. Confirm available organisms for the selected release with `list(census[\"census_data\"].keys())`.\n\n### Gene Metadata (var)\n- `feature_id` (Ensembl gene ID, e.g., \"ENSG00000161798\")\n- `feature_name` (Gene symbol, e.g., \"FOXP2\")\n- `feature_type`\n- `feature_length` (Gene length in base pairs)\n- `nnz`, `n_measured_obs` (availability summaries useful for checking sparsity and coverage)\n\n## Reference Documentation\n\nThis skill includes detailed reference documentation:\n\n### references/census_schema.md\nComprehensive documentation of:\n- Census data structure and organization\n- All available metadata fields\n- Value filter syntax and operators\n- SOMA object types\n- Data inclusion criteria\n\n**When to read:** When you need detailed schema information, full list of metadata fields, or complex filter syntax.\n\n### references/common_patterns.md\nExamples and patterns for:\n- Exploratory queries (metadata only)\n- Small-to-medium queries (AnnData)\n- Large queries (out-of-core processing)\n- PyTorch integration\n- Spatial Census access patterns\n- Scanpy integration workflows\n- Multi-dataset integration\n- Best practices and common pitfalls\n\n**When to read:** When implementing specific query patterns, looking for code examples, or troubleshooting common issues.\n\n## Common Use Cases\n\n### Use Case 1: Explore Cell Types in a Tissue\n```python\nwith cellxgene_census.open_soma() as census:\n    cells = cellxgene_census.get_obs(\n        census, \"homo_sapiens\",\n        value_filter=\"tissue_general == 'lung' and is_primary_data == True\",\n        column_names=[\"cell_type\"]\n    )\n    print(cells[\"cell_type\"].value_counts())\n```\n\n### Use Case 2: Query Marker Gene Expression\n```python\nwith cellxgene_census.open_soma() as census:\n    adata = cellxgene_census.get_anndata(\n        census=census,\n        organism=\"Homo sapiens\",\n        var_value_filter=\"feature_name in ['CD4', 'CD8A', 'CD19']\",\n        obs_value_filter=\"cell_type in ['T cell', 'B cell'] and is_primary_data == True\",\n    )\n```\n\n### Use Case 3: Train Cell Type Classifier\n```python\nimport tiledbsoma as soma\nfrom tiledbsoma_ml import ExperimentDataset, experiment_dataloader\n\nwith cellxgene_census.open_soma() as census:\n    experiment = census[\"census_data\"][\"homo_sapiens\"]\n    with experiment.axis_query(\n        measurement_name=\"RNA\",\n        obs_query=soma.AxisQuery(value_filter=\"is_primary_data == True\"),\n    ) as query:\n        dataset = ExperimentDataset(\n            query=query,\n            layer_name=\"raw\",\n            obs_column_names=[\"cell_type\"],\n            batch_size=128,\n            shuffle=True,\n        )\n        dataloader = experiment_dataloader(dataset)\n\n        for X, obs in dataloader:\n            labels = obs[\"cell_type\"]\n            # Training logic\n            pass\n```\n\n### Use Case 4: Cross-Tissue Analysis\n```python\nwith cellxgene_census.open_soma() as census:\n    adata = cellxgene_census.get_anndata(\n        census=census,\n        organism=\"Homo sapiens\",\n        obs_value_filter=\"cell_type == 'macrophage' and tissue_general in ['lung', 'liver', 'brain'] and is_primary_data == True\",\n    )\n\n    # Analyze macrophage differences across tissues\n    sc.tl.rank_genes_groups(adata, groupby=\"tissue_general\")\n```\n\n## Troubleshooting\n\n### Query Returns Too Many Cells\n- Add more specific filters to reduce scope\n- Use `tissue` instead of `tissue_general` for finer granularity\n- Filter by specific `dataset_id` if known\n- Switch to out-of-core processing for large queries\n\n### Memory Errors\n- Reduce query scope with more restrictive filters\n- Select fewer genes with `var_value_filter`\n- Use out-of-core processing with `axis_query()`\n- Process data in batches\n\n### Duplicate Cells in Results\n- Always include `is_primary_data == True` in filters\n- Check if intentionally querying across multiple datasets\n\n### Gene Not Found\n- Verify gene name spelling (case-sensitive)\n- Try Ensembl ID with `feature_id` instead of `feature_name`\n- Check dataset presence matrix to see if gene was measured\n- Some genes may have been filtered during Census construction\n\n### Version Inconsistencies\n- Always specify `census_version` explicitly\n- Use same version across all analyses\n- Check release notes for version-specific changes\n","tagline":"Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics 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"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":73,"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":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":"pass","label":"OpenAgentSkill usage","detail":"9 views, 0 install copies"},{"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; 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"],"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"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census","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","6d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["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"]},"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":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,"blocked":false,"human_review_required":true,"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"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":77,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: shell or command execution, network or browser access","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: shell or command execution, network or browser access"],"warnings":["Trust score: Good trust signals with a few areas worth checking before rollout.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","High-risk permission hints: Shell or command execution","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"],"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":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate cellxgene-census before installing it in an agent workflow","research","Research agents workflows; Claude Code teams; teams that value GitHub adoption signals"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill cellxgene-census"]},{"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 K-Dense-AI/scientific-agent-skills --skill cellxgene-census"]},{"id":"trust_score","label":"Trust score","status":"warn","score":73,"required_for_auto_install":true,"detail":"Good trust signals with a few areas worth checking before rollout.","evidence":["Strong shortlist","38K GitHub stars","MIT"]},{"id":"audit_score","label":"Audit score","status":"warn","score":84,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":56,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","High-risk permission hints: Shell or command execution"]},{"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":"MIT","evidence":["MIT"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"6d since push","evidence":["6d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":50,"required_for_auto_install":true,"detail":"shell or command execution, network or browser access","evidence":["Shell or command execution: high","Network 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/k-dense-ai-cellxgene-census/evals","api":"/api/agent/evals?slug=k-dense-ai-cellxgene-census","text":"/api/agent/evals?slug=k-dense-ai-cellxgene-census&format=text"}},"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.","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.","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."],"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.","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.","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."],"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"}},"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; 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."]},"coverageTags":["Research","Research agents","agent-skill"]},"audit":{"audit_score":84,"risk_level":"needs_review","risk_label":"Needs review","quality_score":92,"trust_score":73,"maintenance_score":100,"security_score":75,"install_score":92,"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"]},"quality_signals":{"model":"v2","star_score":32.1,"usage_score":0,"review_score":4.95,"metadata_score":3,"freshness_score":15},"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"}],"stacks":[{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"rag-knowledge-base","title":"RAG knowledge base","url":"https://www.openagentskill.com/collections/rag-knowledge-base"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"}],"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","urls":{"web":"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","api":"/api/agent/skills/k-dense-ai-cellxgene-census","install_api":"/api/skills/k-dense-ai-cellxgene-census/install"},"meta":{"created_at":"2026-08-30T13:23:56.678366+00:00","updated_at":"2026-09-01T11:59:28.941454+00:00","agent_friendly":true}}