pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
python-packaging
Create distributable Python packages with proper project structure, setup.py/pyproject.toml, and publishing to PyPI. Use when packaging Python libraries, creating CLI tools, or distributing Python code.
python-performance-optimization
Profile and optimize Python code using cProfile, memory profilers, and performance best practices. Use when debugging slow Python code, optimizing bottlenecks, or improving application performance.
python-testing-patterns
Implement comprehensive testing strategies with pytest, fixtures, mocking, and test-driven development. Use when writing Python tests, setting up test suites, or implementing testing best practices.
pytorch-fsdp
Expert guidance for Fully Sharded Data Parallel training with PyTorch FSDP - parameter sharding, mixed precision, CPU offloading, FSDP2
pytorch-lightning
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
qms-audit-expert
Senior QMS Audit Expert for internal and external quality management system auditing. Provides ISO 13485 audit expertise, audit program management, nonconformity identification, and corrective action verification. Use for internal audit planning, external audit preparation, audit execution, and audit follow-up activities.
quality-documentation-manager
Senior Quality Documentation Manager for comprehensive documentation control and regulatory document review. Provides document management system design, change control, configuration management, and regulatory documentation oversight. Use for document control system implementation, regulatory document review, change management, and documentation compliance verification.
quality-manager-qmr
Senior Quality Manager Responsible Person (QMR) for HealthTech and MedTech companies. Provides overall quality system responsibility, regulatory compliance oversight, management accountability, and strategic quality leadership. Use for quality system governance, regulatory compliance oversight, management responsibility, and quality strategic planning.
quality-manager-qms-iso13485
ISO 13485 Quality Management System specialist for medical device companies. Provides QMS implementation, maintenance, process optimization, and compliance expertise. Use for QMS design, documentation control, management review, internal auditing, corrective actions, and ISO 13485 certification activities.
raffle-winner-picker
Picks random winners from lists, spreadsheets, or Google Sheets for giveaways, raffles, and contests. Ensures fair, unbiased selection with transparency.
rag-implementation
Build Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.
ray-data
Scalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing, multi-modal data loading, or distributed ETL pipelines.
ray-train
Distributed training orchestration across clusters. Scales PyTorch/TensorFlow/HuggingFace from laptop to 1000s of nodes. Built-in hyperparameter tuning with Ray Tune, fault tolerance, elastic scaling. Use when training massive models across multiple machines or running distributed hyperparameter sweeps.
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
react-hook-form-zod
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react-modernization
Upgrade React applications to latest versions, migrate from class components to hooks, and adopt concurrent features. Use when modernizing React codebases, migrating to React Hooks, or upgrading to latest React versions.
react-native-expo
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reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
readme-updater
Keep README files current with project changes. Use when project structure changes, features added, or setup instructions modified. Suggests README updates based on code changes. Triggers on significant project changes, new features, dependency changes.
regulatory-affairs-head
Senior Regulatory Affairs Manager expertise for HealthTech and MedTech companies. Provides strategic regulatory guidance, submission management, regulatory pathway analysis, global compliance coordination, and cross-functional team leadership. Use for regulatory strategy development, submission planning, regulatory risk assessment, and team coordination activities.
reportlab
PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.
research-grants
Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
research-lookup
Look up current research information using Perplexity's Sonar Pro or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
risk-management-specialist
Senior Risk Management specialist for medical device companies implementing ISO 14971 risk management throughout product lifecycle. Provides risk analysis, risk evaluation, risk control, and post-production information analysis. Use for risk management planning, risk assessments, risk control verification, and risk management file maintenance.
rwkv-architecture
RNN+Transformer hybrid with O(n) inference. Linear time, infinite context, no KV cache. Train like GPT (parallel), infer like RNN (sequential). Linux Foundation AI project. Production at Windows, Office, NeMo. RWKV-7 (March 2025). Models up to 14B parameters.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
scholar-evaluation
Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill should be used when assessing research papers, evaluating literature reviews, scoring research methodologies, analyzing scientific writing quality, or applying structured evaluation criteria to academic work. Provides comprehensive assessment across multiple dimensions including problem formulation, literature review, methodology, data collection, analysis, results interpretation, and scholarly writing quality.
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
scientific-critical-thinking
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
scientific-schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with iterative refinement. AI generation is the default method for all diagram types. Generates high-fidelity images with automatic quality review. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
scientific-writing
Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scikit-learn
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
scikit-survival
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.
scvi-tools
This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.
seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
secret-scanner
Detect exposed secrets, API keys, credentials, and tokens in code. Use before commits, on file saves, or when security is mentioned. Prevents accidental secret exposure. Triggers on file changes, git commits, security checks, .env file modifications.
security-auditor
Continuous security vulnerability scanning for OWASP Top 10, common vulnerabilities, and insecure patterns. Use when reviewing code, before deployments, or on file changes. Scans for SQL injection, XSS, secrets exposure, auth issues. Triggers on file changes, security mentions, deployment prep.
senior-architect
Comprehensive software architecture skill for designing scalable, maintainable systems using ReactJS, NextJS, NodeJS, Express, React Native, Swift, Kotlin, Flutter, Postgres, GraphQL, Go, Python. Includes architecture diagram generation, system design patterns, tech stack decision frameworks, and dependency analysis. Use when designing system architecture, making technical decisions, creating architecture diagrams, evaluating trade-offs, or defining integration patterns.
senior-backend
Comprehensive backend development skill for building scalable backend systems using NodeJS, Express, Go, Python, Postgres, GraphQL, REST APIs. Includes API scaffolding, database optimization, security implementation, and performance tuning. Use when designing APIs, optimizing database queries, implementing business logic, handling authentication/authorization, or reviewing backend code.
senior-computer-vision
World-class computer vision skill for image/video processing, object detection, segmentation, and visual AI systems. Expertise in PyTorch, OpenCV, YOLO, SAM, diffusion models, and vision transformers. Includes 3D vision, video analysis, real-time processing, and production deployment. Use when building vision AI systems, implementing object detection, training custom vision models, or optimizing inference pipelines.
senior-data-engineer
World-class data engineering skill for building scalable data pipelines, ETL/ELT systems, and data infrastructure. Expertise in Python, SQL, Spark, Airflow, dbt, Kafka, and modern data stack. Includes data modeling, pipeline orchestration, data quality, and DataOps. Use when designing data architectures, building data pipelines, optimizing data workflows, or implementing data governance.
senior-data-scientist
World-class data science skill for statistical modeling, experimentation, causal inference, and advanced analytics. Expertise in Python (NumPy, Pandas, Scikit-learn), R, SQL, statistical methods, A/B testing, time series, and business intelligence. Includes experiment design, feature engineering, model evaluation, and stakeholder communication. Use when designing experiments, building predictive models, performing causal analysis, or driving data-driven decisions.
senior-devops
Comprehensive DevOps skill for CI/CD, infrastructure automation, containerization, and cloud platforms (AWS, GCP, Azure). Includes pipeline setup, infrastructure as code, deployment automation, and monitoring. Use when setting up pipelines, deploying applications, managing infrastructure, implementing monitoring, or optimizing deployment processes.
senior-frontend
Comprehensive frontend development skill for building modern, performant web applications using ReactJS, NextJS, TypeScript, Tailwind CSS. Includes component scaffolding, performance optimization, bundle analysis, and UI best practices. Use when developing frontend features, optimizing performance, implementing UI/UX designs, managing state, or reviewing frontend code.
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