Results for “mining”

Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/comorbidity, and label change tracking. Use for post-market safety surveillance, AE signal investigation, drug-AE association strength scoring, and pharmacovigilance reports.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Improve how interfaces use photos, screenshots, icons, illustrations, and user-uploaded media so visuals support clarity instead of undermining it. Use when the user mentions images, screenshots, background photos, hero images, icon sizing, user-uploaded media, crops, overlays, or image readability.

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Interactive Flutter Widget implementation assistant that guides you through widget implementation decisions by asking structured questions about state management, widget type (screen/component), and state sharing. Use this skill when you need help determining the appropriate Flutter widget architecture for your implementation.

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Orchestrate continual learning by delegating transcript mining and AGENTS.md updates to `agents-memory-updater`.

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Tactical fast path: turn a small problem, bug report, edit request, or narrow refactor into three deliverables — a brief change-spec (docs/specs/), a detailed implementation-ready plan (docs/plans/), and a TODO.md with agent-pickable tasks and milestones. Load when the user describes a tactical problem and wants quick planning artifacts, says "plan this change", "create a TODO", "write a plan for this", "problem to plan", "break this into tasks for agents", "I want to change X — plan it", or when process-decomposer routes here after determining the user needs lightweight planning deliverables. Also triggers on "create tasks from this problem", "make this actionable", or "turn this into a plan agents can execute". For feature-sized work that needs an executable spec + constitution + cross-check gate, route to `spec-driven-development` (or `feature-spec`) instead.

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Generate 5–10 business idea candidates from a blank page or a founder's domain context — using pain mining, jobs-to-be-done, trend × capability mapping, constraint relaxation, adjacency search, and founder-market-fit prompts. Each candidate is a structured idea card (segment, JTBD, current alternative, why-now, distribution wedge, monetisation, "feels like"). Load when the user asks to generate business ideas, brainstorm startup ideas, find ideas to work on, says "what business should I start", "give me startup ideas", "I don't know what to build", "ideate ventures", "blank-page idea generation", "find me a startup idea", "explore business opportunities". Sub-skill of `venture-exploration`. Hard-bans "Uber for X" / "AI for X" with no specific JTBD, "everyone" segments, and idea cards missing any of the 7 required fields. Does NOT design or evaluate ideas generated — for that use `idea-evaluation`.

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Debug LangChain and LangGraph agents by fetching execution traces from LangSmith Studio. Use when debugging agent behavior, investigating errors, analyzing tool calls, checking memory operations, or examining agent performance. Automatically fetches recent traces and analyzes execution patterns. Requires langsmith-fetch CLI installed.

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Workflow for classifying AI Matrx server log lines in features/server-logs/log-rules.ts. Use when examining raw server logs, new [ModuleName] bracket tokens appear unclassified, log categories are wrong, or adding module recognition to the log viewer.

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Analyze context and decide on continuation via Stop hook. Use when determining if work should continue, analyzing completion status, making continuation decisions, or implementing the Two-Claude pattern.

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When the user requests to add academic papers to a BibTeX bibliography file while maintaining format consistency and sourcing from appropriate repositories. This skill handles 1) Reading existing BibTeX files to understand formatting conventions, 2) Searching for academic papers across multiple sources (OpenReview for conference papers, arXiv for preprints), 3) Extracting proper BibTeX metadata from conference pages or arXiv entries, 4) Determining appropriate citation format (@article vs @inproceedings) based on publication venue, 5) Appending new entries while preserving existing file structure and formatting. Triggers include requests to 'add to ref.bib', 'update bibliography', 'cite papers', or when working with academic reference files.

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Debug LangChain and LangGraph agents by fetching execution traces from LangSmith Studio. Use when debugging agent behavior, investigating errors, analyzing tool calls, checking memory operations, or examining agent performance. Automatically fetches recent traces and analyzes execution patterns. Requires langsmith-fetch CLI installed.

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Detects typosquatting attacks in npm and PyPI package registries by analyzing package name similarity using Levenshtein distance and other string metrics, examining publish date heuristics to identify recently created packages mimicking established ones, and flagging download count anomalies where suspicious packages have disproportionately low usage compared to their legitimate targets. The analyst queries the PyPI JSON API and npm registry API to gather package metadata for automated comparison. Activates for requests involving package typosquatting detection, dependency confusion analysis, malicious package identification, or software supply chain threat hunting in package registries.

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Responds to malware infections across enterprise endpoints by identifying the malware family, determining infection vectors, assessing spread, and executing eradication procedures. Covers the full lifecycle from detection through containment, analysis, removal, and recovery. Activates for requests involving malware response, malware eradication, trojan removal, worm containment, malware triage, or infected endpoint remediation.

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Builds comprehensive identity governance and lifecycle management processes including joiner-mover-leaver automation, role mining, access request workflows, periodic recertification, and orphaned account remediation using IGA platforms. Activates for requests involving identity lifecycle management, JML processes, role-based access provisioning, or identity governance program design.

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Analyze the NTFS Master File Table ($MFT) to recover metadata and content of deleted files by examining MFT record entries, $LogFile, $UsnJrnl, and MFT slack space using MFTECmd, analyzeMFT, and X-Ways Forensics.

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External recon for software supply-chain attack surface — package-namespace squatting candidates, dependency-confusion vulnerabilities, GitHub Actions injection openings, container image registry exposure, SBOM mining, internal-package-name leakage, and CI/CD configuration exposure. Reconnaissance and identification ONLY — actual package publishing / typosquat attacks are EXTERNAL-OFFENSIVE and require explicit written sign-off because they can affect the entire npm/PyPI ecosystem. Use when the target has a public GitHub org, when their build artifacts/SBOMs are reachable, when their docker images are on Docker Hub/GHCR, or when you find internal package names in their JS bundles.

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Penetration test and red team report writing methodology. Covers executive summary structuring (risk-led narrative for non-technical readers), technical finding format (title, severity, affected scope, narrative, reproduction steps, impact, remediation, references), CVSS v3.1 / v4.0 scoring with vector justification, OWASP risk rating, evidence hygiene (redacting credentials, hashing client data, time-stamping every action), screenshot and PoC artifact management, finding chain narratives, scope/limitations/assumptions documentation, retest evidence and remediation tracking, deliverable formats (PDF, DOCX, HTML, JSON for SIEM ingestion), client-customer-deliverable separation, and common report mistakes (over-CVSSing, undermining the triager, missing the 'so what'). Use at the end of an engagement when authoring a deliverable, when restructuring a draft for executive readability, or when establishing a reusable report template for a consulting practice.

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