{"slug":"clawbio-celltype-specificity-profiler","name":"celltype-specificity-profiler","description":"Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.","long_description":"---\nname: celltype-specificity-profiler\ndescription: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.\nlicense: MIT\nmetadata:\n  version: \"0.1.0\"\n  author: Jacky Siu\n  domain: single-cell\n  tags:\n    - scrna\n    - single-cell\n    - specificity\n    - tau\n    - bimodality\n    - target-prioritization\n    - marker-gene\n    - h5ad\n  inputs:\n    - name: atlas\n      type: file\n      format:\n        - h5ad\n      description: Annotated single-cell expression matrix (log-normalized X; cell-type labels in an obs column). In the chain, this is the output of upstream scrna-embedding.\n      required: false\n    - name: gene\n      type: string\n      format:\n        - txt\n      description: HGNC gene symbol to profile (e.g. CD276). Required unless --demo.\n      required: false\n  outputs:\n    - name: profile\n      type: file\n      format:\n        - json\n      description: Specificity profile — tau, bimodality coefficient, ranked cell types, per-cell-type stats, optional trial prior.\n    - name: per_celltype\n      type: file\n      format:\n        - csv\n      description: Tidy per-cell-type expression table for plotting.\n  dependencies:\n    python: \">=3.10\"\n    packages:\n      - scanpy\n      - anndata\n      - numpy>=1.23\n      - scipy>=1.9\n      - pandas>=2.0\n  demo_data:\n    - path: examples/expected_demo_profile.json\n      description: Reference output of `--demo` on scanpy's bundled real pbmc3k dataset (gene MS4A1).\n  endpoints:\n    cli: python skills/celltype-specificity-profiler/profiler.py --gene {gene} --atlas {atlas} --output {output_dir}\n  openclaw:\n    requires:\n      bins:\n        - python3\n    always: false\n    emoji: \"🎯\"\n    homepage: https://github.com/ClawBio/ClawBio\n    os:\n      - darwin\n      - linux\n    install:\n      - kind: uv\n        package: scanpy\n      - kind: uv\n        package: anndata\n      - kind: uv\n        package: numpy\n      - kind: uv\n        package: scipy\n      - kind: uv\n        package: pandas\n    trigger_keywords:\n      - cell-type specificity\n      - cell type specificity\n      - specificity index\n      - tau index\n      - tau specificity\n      - bimodality\n      - bimodality coefficient\n      - cell-type-specific expression\n      - expression specificity\n      - marker gene specificity\n---\n\n# 🎯 Cell-Type Specificity Profiler\n\nYou are **Cell-Type Specificity Profiler**, a specialised ClawBio agent for single-cell analysis. Your role is to quantify, for a single gene, how cell-type-specific its expression is across an annotated atlas.\n\n## Trigger\n\n**Fire this skill when the user says any of:**\n- \"how cell-type-specific is <gene>?\"\n- \"compute the tau specificity index for <gene>\"\n- \"is <gene> a broad or restricted marker?\"\n- \"which cell types express <gene>, and is its expression bimodal?\"\n- \"expression specificity / bimodality coefficient for my target\"\n- \"profile target specificity (optionally with the trial-success prior)\"\n\n**Do NOT fire when:**\n- The user wants to *build* the embedding / integrate batches / cluster cells → that is `scrna-embedding` or `scrna-orchestrator`.\n- The user wants differential expression between conditions → that is `rnaseq-de` / `proteomics-de`.\n- The user wants generic target evidence (GWAS, tractability, known drugs) rather than a single-cell specificity metric → that is `omics-target-evidence-mapper` / `target-validation-scorer`.\n\n**Design note:** This skill consumes an already-annotated matrix and returns one focused metric set. It does not fetch, embed, or cluster.\n\n## Why This Exists\n\nTarget prioritization, off-target safety triage, and marker-gene discovery all hinge on cell-type specificity. ClawBio's existing single-cell skills (`scrna-embedding`, `omics-target-evidence-mapper`) embed and annotate cells, but **none return a per-gene specificity metric**.\n\n- **Without it**: Users hand-roll pseudobulk aggregation and ad-hoc specificity scores, with no standard tau / bimodality contract for downstream skills.\n- **With it**: One command returns a clean specificity profile (`tau`, `bimodality_coefficient`, ranked cell types) plus a tidy table, ready for `target-validation-scorer` and `clinical-trial-finder`.\n- **Why ClawBio**: It is a **pure analytic transform — it does not fetch data**. Data access stays upstream (`scrna-embedding` pulls real atlases from CELLxGENE Census); this skill computes metrics on the matrix it is handed, keeping it a clean, chainable citizen rather than a competing data connector, and preserves the reproducibility-bundle contract.\n\nIt implements the two complementary single-cell features from *The Virtual Biotech* (Zhang et al., 2026): cell-type-specific targets progress further in clinical trials with fewer adverse events. The bimodality coefficient is a cross-domain transfer from psychometrics, only moderately correlated with tau (ρ≈0.54), so the two carry complementary signal. The paper's trial-success scoring is an *optional* layer (`--trial-prior`), so the core capability is not locked to one preprint's coefficients.\n\n## Core Capabilities\n\n1. **Tau Specificity Index**: Yanai et al. 2005 index over pseudobulk per-cell-type means, in [0, 1] (0 = ubiquitous → 1 = single-cell-type restricted).\n2. **Bimodality Coefficient**: Sarle's BC (bias-corrected skewness/kurtosis) over expressing cells — an \"on/off\" expression signal.\n3. **Cell-Type Ranking**: Top expressing cell types with mean expression and fraction expressing, plus full per-cell-type stats.\n4. **Optional Trial Prior**: With `--trial-prior`, attach the published Zhang et al. 2026 odds ratios (labelled, correlational).\n5. **Reproducibility Bundle**: Emit `commands.sh`, `environment.yml`, and SHA-256 checksums.\n\n## Scope\n\n**One skill, one task.** This skill computes per-gene cell-type specificity metrics from an annotated matrix and nothing else. It does not fetch data, embed, cluster, annotate, or run differential expression — those belong to other skills.\n\n## Input Formats\n\n| Format | Extension | Required Fields | Example |\n|--------|-----------|-----------------|---------|\n| AnnData annotated matrix | `.h5ad` | Log-normalized (non-negative) expression in `X`; cell-type labels in an `obs` column; gene in `var` index | `lung_atlas.h5ad` |\n| Demo mode | n/a | none — uses scanpy's bundled, real `pbmc3k` dataset | `--demo` |\n\nIn the chain, the `.h5ad` is the **output of upstream `scrna-embedding`**, not fetched here.\n\n## Workflow\n\n1. **Load**: Read the `.h5ad` (or `--demo`); resolve the cell-type `obs` column (`--cell-type-key`, auto-detected from common names).\n2. **Resolve gene**: Map the symbol against the atlas `var` index (small alias map, e.g. CD276 ↔ B7-H3); fail loudly on a genuinely missing symbol rather than returning zeros. *(Prescriptive.)*\n3. **Subset**: If `--tissue` is given, restrict to that label; error if absent. *(Prescriptive.)*\n4. **Aggregate & score**: Pseudobulk mean expression per cell type → `tau`; bimodality coefficient over expressing cells; set `low_expression` when the gene is expressed in <1% of cells. *(Prescriptive.)*\n5. **Generate**: Write `profile.json`, `per_celltype.csv`, and the reproducibility bundle; if `--trial-prior`, attach the labelled odds ratios. *(Prescriptive.)*\n\n## CLI Reference\n\n```bash\n# Standard usage — profile a gene against your own atlas\npython skills/celltype-specificity-profiler/profiler.py \\\n  --gene CD276 --atlas lung_atlas.h5ad --output <report_dir>\n\n# Restrict to a tissue and attach the paper's trial-success prior\npython skills/celltype-specificity-profiler/profiler.py \\\n  --gene CD276 --atlas lung_atlas.h5ad --tissue lung --trial-prior --output <report_dir>\n\n# Demo mode (real scanpy-bundled pbmc3k; default gene MS4A1)\npython skills/celltype-specificity-profiler/profiler.py --demo --output <report_dir>\n\n# Via ClawBio runner\npython clawbio.py run celltype-specificity-profiler --demo\n```\n\n## Demo\n\n```bash\npython clawbio.py run celltype-specificity-profiler --demo\n```\n\nThe demo runs on scanpy's bundled, **real** `pbmc3k` 10x dataset (2,638 cells, annotated cell types) — no synthetic data. The default gene `MS4A1` is a canonical B-cell marker, so it scores as highly cell-type-specific. A reference of this output ships at `examples/expected_demo_profile.json`.\n\n## Algorithm / Methodology\n\n1. Load atlas; resolve gene against `var` (with alias map) and subset (and `--tissue` if given).\n2. Aggregate to **pseudobulk mean expression per cell type** (expects log-normalized, non-negative input).\n3. **tau** = Σᵢ(1 − xᵢ/x_max) / (n − 1) over n cell types; xᵢ = mean expression in cell type i. NaN for n < 2. Following Zhang et al. 2026, cell types with **fewer than 20 cells are excluded** from the tau computation (their pseudobulk means are unreliable and, via the max-normalization, can distort tau); they remain in `per_celltype_stats`, and the profile records `n_cell_types_used_for_tau` / `n_cell_types_excluded_small`.\n4. **Bimodality coefficient** = (g1² + 1) / (g2 + 3·(n−1)²/((n−2)(n−3))), g1/g2 = bias-corrected sample skewness/excess kurtosis over expressing cells. NaN for n < 4 or zero variance.\n5. Rank cell types by mean expression; if `--trial-prior`, label tau against `tau_threshold` and attach the published ORs.\n\n**Key thresholds / parameters**:\n- `TAU_THRESHOLD = 0.69` — tau > 0.69 → \"cell-type-specific\". This is **not** a universal constant: Zhang et al. 2026 (Extended Methods) derived it as the midpoint of a K-means (k=2) split of *their trial-level* tau distribution, so it is cohort-specific. Treat continuous `tau` as the real output and recalibrate the cut on your own distribution if you binarize.\n- `MIN_CELLS_FOR_TAU = 20` — cell types with <20 cells are dropped from the tau computation (source: Zhang et al. 2026).\n- `LOW_EXPRESSION_FRACTION = 0.01` — gene expressed in <1% of cells flags an unreliable BC.\n- Trial-prior odds ratios: phase I→II OR 1.27 (95% CI 1.22–1.33), primary-endpoint OR 1.11 (95% CI 1.09–1.14) — verified verbatim against Zhang et al. 2026 Results.\n\n## Example Queries\n\n- \"How cell-type-specific is CD276 in this lung atlas?\"\n- \"Compute the tau specificity index for MS4A1\"\n- \"Which cell types express B7-H3, and is its expression bimodal?\"\n- \"Profile this gene's specificity and give me the trial-success prior\"\n\n## Example Output\n\n`profile.json` (demo, `--demo --trial-prior`, abbreviated):\n\n```json\n{\n  \"skill\": \"celltype-specificity-profiler\",\n  \"gene\": \"MS4A1\",\n  \"atlas\": \"pbmc3k (10x, real; scanpy bundled)\",\n  \"tau\": 0.956,\n  \"tau_threshold\": 0.69,\n  \"tau_threshold_note\": \"cohort-specific K-means(k=2) midpoint of the trial-level tau distribution in Zhang et al. 2026 (tau=0.69); an interpretive default, not a universal cutoff\",\n  \"n_cell_types_used_for_tau\": 7,\n  \"n_cell_types_excluded_small\": 1,\n  \"bimodality_coefficient\": 0.4936,\n  \"interpretation\": \"cell-type-specific (tau > 0.69)\",\n  \"low_expression\": false,\n  \"top_cell_types\": [\n    {\"cell_type\": \"B cells\", \"mean_expr\": 0.993, \"pct_expressing\": 0.8596},\n    {\"cell_type\": \"FCGR3A+ Monocytes\", \"mean_expr\": 0.0601, \"pct_expressing\": 0.0867}\n  ],\n  \"trial_prior\": {\n    \"note\": \"Odds ratios from Zhang et al. 2026 (bioRxiv 10.64898/2026.02.23.707551)\",\n    \"phase_I_to_II_OR\": 1.27,\n    \"primary_endpoint_OR\": 1.11,\n    \"lower_AE_rate\": true\n  }\n}\n```\n\n`per_celltype.csv`:\n\n```csv\ncell_type,mean_expr,median_expr,pct_expressing,n_cells\nB cells,0.993,1.0986,0.8596,342\nFCGR3A+ Monocytes,0.0601,0.0,0.0867,150\n```\n\n*ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses.*\n\n## Output Structure\n\n```text\noutput_directory/\n├── profile.json              # specificity contract: tau, bimodality, ranked + per-cell-type stats, optional trial_prior\n├── per_celltype.csv          # tidy per-cell-type table\n└── reproducibility/\n    ├── commands.sh            # exa","tagline":"Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.","category":"research","tags":["agent-skill"],"author":"ClawBio","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github candidate review","sourceDetail":"ClawBio/ClawBio","creatorName":"ClawBio","creatorUrl":"https://github.com/ClawBio","sourceUrl":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/clawbio-celltype-specificity-profiler#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":1125,"forks":259,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":44.91},"quality":{"score":78,"tier":"strong","label":"Strong","summary":"Solid option that is likely worth shortlisting for production workflows.","signals":[{"label":"GitHub stars","value":"1.1K","tone":"positive"},{"label":"Freshness","value":"1d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT","tone":"neutral"}],"warnings":["The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users."]},"trust":{"version":"trust-score-v5","score":66,"base_score":74,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.","recommendedAction":"Run only in a sandbox and compare close alternatives before using it for real work.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["66/100 Trust Score v5","74/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","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"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":86,"weight":0.13,"status":"pass","detail":"1.1K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":83,"weight":0.08,"status":"pass","detail":"1.1K stars, 259 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"1d 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":64,"weight":0.12,"status":"info","detail":"command execution surface, network or browser surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler"},{"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":48,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler"},{"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":"1.1K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"1.1K stars, 259 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"1d 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":"info","label":"Dependency/runtime risk","detail":"command execution surface, network or browser surface"},{"status":"pass","label":"Install availability","detail":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Meaningful GitHub adoption signal","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. 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This could confuse users.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":74,"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":74,"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":86,"weight":0.13,"status":"pass","detail":"1.1K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":83,"weight":0.08,"status":"pass","detail":"1.1K stars, 259 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"1d 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":64,"weight":0.12,"status":"info","detail":"command execution surface, network or browser surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler"},{"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":48,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler"},{"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":"1.1K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"1.1K stars, 259 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"1d 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":"info","label":"Dependency/runtime risk","detail":"command execution surface, network or browser surface"},{"status":"pass","label":"Install availability","detail":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Meaningful GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. 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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","53/100 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":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution","Permission surface may require sandboxing"],"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","53/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":73,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: shell or command execution, filesystem or document access","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: shell or command execution, filesystem or document 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. 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This could confuse users.","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document 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 celltype-specificity-profiler 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 ClawBio/ClawBio --skill celltype-specificity-profiler"]},{"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 ClawBio/ClawBio --skill celltype-specificity-profiler"]},{"id":"trust_score","label":"Trust score","status":"warn","score":74,"required_for_auto_install":true,"detail":"Good trust signals with a few areas worth checking before rollout.","evidence":["Strong shortlist","1.1K GitHub stars","MIT"]},{"id":"audit_score","label":"Audit score","status":"warn","score":81,"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":53,"required_for_auto_install":true,"detail":"Sparse or mixed signals. 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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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" as a Claude Code skill from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler. 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. 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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":81,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document 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":78,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"1d 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 `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review"],"agent_contract":{"task_input":"Use celltype-specificity-profiler 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: 74/100 Strong shortlist","Audit: 81/100 Needs review","Safety: 53/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"clawbio-celltype-specificity-profiler (celltype-specificity-profiler)","install_command":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","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":"clawbio-celltype-specificity-profiler","task":"Use celltype-specificity-profiler 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/clawbio-celltype-specificity-profiler","api":"https://www.openagentskill.com/api/agent/skills/clawbio-celltype-specificity-profiler","audit":"https://www.openagentskill.com/skills/clawbio-celltype-specificity-profiler/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=clawbio-celltype-specificity-profiler&task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/clawbio-celltype-specificity-profiler/install","manifest":"https://www.openagentskill.com/api/registry/manifest/clawbio-celltype-specificity-profiler"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"clawbio-celltype-specificity-profiler","name":"celltype-specificity-profiler","description":"Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.","category":"research","url":"https://www.openagentskill.com/skills/clawbio-celltype-specificity-profiler","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler","github_repo":"ClawBio/ClawBio"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Move data between tools","Transform files"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","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 clawbio-celltype-specificity-profiler"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"celltype-specificity-profiler\" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler. 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" as a Claude Code skill from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler. 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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/clawbio-celltype-specificity-profiler/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/clawbio-celltype-specificity-profiler"},"trust":{"score":74,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"1.1K GitHub stars","repoActivity":"1.1K stars, 259 forks","lastPushed":"1d since push","license":"MIT","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler","install":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document 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 `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document 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":81,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document 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":78,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"1d 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 `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review"],"agent_contract":{"task_input":"Use celltype-specificity-profiler 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: 74/100 Strong shortlist","Audit: 81/100 Needs review","Safety: 53/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"clawbio-celltype-specificity-profiler (celltype-specificity-profiler)","install_command":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","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":"clawbio-celltype-specificity-profiler","task":"Use celltype-specificity-profiler 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/clawbio-celltype-specificity-profiler","api":"https://www.openagentskill.com/api/agent/skills/clawbio-celltype-specificity-profiler","audit":"https://www.openagentskill.com/skills/clawbio-celltype-specificity-profiler/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=clawbio-celltype-specificity-profiler&task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20celltype-specificity-profiler%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/clawbio-celltype-specificity-profiler/install","manifest":"https://www.openagentskill.com/api/registry/manifest/clawbio-celltype-specificity-profiler"}},"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":"workflow-automation","title":"Workflow automation"},{"slug":"github-automation","title":"GitHub automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":1125,"starsLabel":"1.1K","forks":259,"license":"MIT","qualityScore":78,"trustScore":74,"auditScore":81},"maintenance":{"status":"fresh","label":"1d since push","daysSincePush":1,"lastPushedAt":"2026-09-04T10:49:46+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Permission surface may require sandboxing","The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access"]},"coverageTags":["Research","Research agents","agent-skill"]},"audit":{"audit_score":81,"risk_level":"needs_review","risk_label":"Needs review","quality_score":78,"trust_score":74,"maintenance_score":100,"security_score":76,"install_score":92,"warnings":["Permission surface may require sandboxing","The `atlas` input is marked `required: false` in metadata, but the description and CLI imply it is required unless `--demo` is used. This could confuse users.","The output description mentions an 'optional trial prior' but no input parameter for it is defined in the metadata or CLI.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"quality_signals":{"model":"v2","star_score":21.36,"usage_score":0,"review_score":5.55,"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":"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"},{"slug":"data-analysis","title":"Data analysis","url":"https://www.openagentskill.com/use-cases/data-analysis"}],"stacks":[{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"frontend-product-ui","title":"Frontend and UI","url":"https://www.openagentskill.com/collections/frontend-product-ui"}],"install":"npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler","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 clawbio-celltype-specificity-profiler","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 \"celltype-specificity-profiler\" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler. 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" as a Claude Code skill from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler. 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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 \"celltype-specificity-profiler\" from https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler 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: Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding. 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\":\"clawbio-celltype-specificity-profiler\",\"task\":\"Install celltype-specificity-profiler\",\"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/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler","github_repo":"ClawBio/ClawBio","version":"1.0.0","license":"MIT","urls":{"web":"https://www.openagentskill.com/skills/clawbio-celltype-specificity-profiler","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/celltype-specificity-profiler","api":"/api/agent/skills/clawbio-celltype-specificity-profiler","install_api":"/api/skills/clawbio-celltype-specificity-profiler/install"},"meta":{"created_at":"2026-09-04T14:55:26.880294+00:00","updated_at":"2026-09-04T14:55:27.085393+00:00","agent_friendly":true}}