clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
clinicaltrials-database
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
eval-harness-updater
Refresh evaluation harnesses with live/fallback parser reliability, SLO gates, and regression checks.
exa-monitor
Scheduled Exa web search monitor. Uses CronCreate to search configured topics every 4 hours via mcp__Exa__web_search_exa, deduplicates URLs via MemoryRecord, and stores summaries for morning briefing integration.
expo-framework-rule
Expo Framework-specific guidelines. Includes best practices for Views, Blueprints, and Extensions.
expo-mobile-app-rule
Specifies best practices and conventions for Expo-based mobile app development.
feature-flag-management
Feature flag lifecycle management -- safe feature toggling, gradual rollouts, A/B testing patterns, flag cleanup strategies, and technical debt prevention. Covers LaunchDarkly, Unleash, OpenFeature, and custom implementations.
feedback-analysis
Customer feedback analysis — sentiment detection, NPS/CSAT frameworks, feature request clustering, support ticket triage, churn signal detection, and feedback-to-roadmap translation
figma
Figma design-to-code workflow. Read Figma files, inspect components, extract design tokens, and translate designs to implementation. Use when working with Figma designs, extracting styles, or building design systems.
citation-management
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
cirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
chembl-database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
frontend-expert
Frontend development expert including UI/UX patterns, responsive design, and accessibility
framework-context
Load and synthesize framework architecture context for reflection and planning tasks.
forum-monitor
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form-validation-with-zod
Enforces the use of Zod for form validation throughout the project.
form-and-actions-in-sveltekit
Describes Form and Actions implementations.
fix-review
Verify fix commits address security findings without introducing new bugs or regressions. Analyzes diffs for anti-patterns like removed validation, weakened access control, reduced error handling, reordered external calls, and changed integer operations. Generates structured FIX_REVIEW_REPORT with finding status tracking.
fintech-engineer
Fintech engineering expertise — payment processing (Stripe, Plaid), PCI DSS compliance, financial data modeling (double-entry bookkeeping), fraud detection patterns, bank-grade security (encryption, tokenization), open banking APIs, cryptocurrency/blockchain integration, regulatory compliance (KYC/AML), and idempotent financial transaction design. Use for payment systems, banking apps, trading platforms, and fintech infrastructure.
cron-decision
Decision framework for agents to determine WHEN and WHETHER to use Claude Code's native cron scheduler (CronCreate/CronList/CronDelete) vs OS cron, GitHub Actions, or simple Task() delegation.
cron-runner
Background orchestrator that drains the system-wide cron-actions-queue.jsonl queue safely, preventing LLM context pollution in the primary router.
data-expert
Data processing expert including parsing, transformation, and validation
database-architect
Database design and optimization specialist. Schema design, query optimization, indexing strategies, data modeling, and migration planning for relational and NoSQL databases.
database-expert
Database expert including Prisma, Supabase, SQL, and NoSQL patterns
de-sloppify
Two-agent cleanup pattern. Implementer works freely, then a dedicated cleanup agent removes unused imports, console.logs, commented-out code, dead code, and formatting issues. Produces a diff of what was cleaned.
debug-log-analysis
Structured debug log analysis for Claude Code sessions — auto-discovers most recent log, runs reducer, extracts error patterns, correlates with full log, produces observability report. Fills 5 identified gaps: hook error body capture, agent identity, file path tracking, stall correlation, success visibility.
debugging
Systematic 4-phase debugging with root cause investigation. Use when fixing bugs to prevent random fixes.
deep-research
Multi-step autonomous research methodology for deep investigation tasks with structured synthesis
dependency-analyzer
Analyzes project dependencies, detects outdated packages, identifies breaking changes, and suggests safe update strategies. Helps maintain dependency health and security.
design-and-user-experience-guidelines
Specifies design and user experience guidelines, including dark mode compatibility, responsive design, performance optimization, modern UI, and accessibility. This rule promotes a user-friendly and vi
design-systems
Design system lookup, CSS best practices, and AI-driven UI component generation via MCP tools
diagram-generator
Generates architecture, database, and system diagrams using Mermaid syntax. Creates visual representations of system architecture, database schemas, component relationships, data flows, and standalone HTML exports.
differential-review
Perform security-focused review of code diffs and pull requests, identifying newly introduced vulnerabilities, security regressions, and unsafe patterns in changed code.
doc-generator
Generates comprehensive documentation from code, APIs, and specifications. Creates API documentation, developer guides, architecture docs, and user manuals with examples and tutorials.
docker-compose
Docker Compose container orchestration and management. Manage multi-container applications, services, networks, and volumes. Use for local development, testing, and orchestration of containerized applications.
filesystem
File system operations guidance - read, write, search, and manage files using Claude Code's built-in tools.
dry-principle
This rule enforces the Don't Repeat Yourself principle to avoid code duplication and improve maintainability.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
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