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.
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.
q
World Q Skill
qiskit
Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.
quillen-model
Quillen model categories: (C,W,F) structures.
qutip
Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics.
r
World R Skill
r2frida
Dynamic instrumentation bridge — radare2 static analysis meets Frida runtime hooking via r2frida:// URI
rank-polymorphism
'APL/BQN rank polymorphism: implicit iteration via array rank, no explicit
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.
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
reality-tech
Reality tech umbrella for AR/VR/XR. Choose the right stack (WebXR/OpenXR/Unity/Unreal) and ship with strong defaults for comfort, performance, and privacy.
ReasoningBank with AgentDB
Implement ReasoningBank adaptive learning with AgentDB's 150x faster vector database. Includes trajectory tracking, verdict judgment, memory distillation, and pattern recognition. Use when building self-learning agents, optimizing decision-making, or implementing experience replay systems.
ReasoningBank Intelligence
Implement adaptive learning with ReasoningBank for pattern recognition, strategy optimization, and continuous improvement. Use when building self-learning agents, optimizing workflows, or implementing meta-cognitive systems.
yoneda-embedding
Yoneda: C → [Cᵒᵖ, Set] fully faithful.
reasoningbank-with-agentdb
ReasoningBank adaptive learning with AgentDB vector backend. Trajectory tracking, verdict judgment, memory distillation. Triggers: reasoningbank, agentdb, adaptive learning, experience replay, trajectory tracking.
refactoring-playbook
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referral-program
When the user wants to create, optimize, or analyze a referral program, affiliate program, or word-of-mouth strategy. Also use when the user mentions 'referral,' 'affiliate,' 'ambassador,' 'word of mouth,' 'viral loop,' 'refer a friend,' or 'partner program.' This skill covers program design, incentive structure, and growth optimization.
relational-thinking
Intent taxonomy and morphisms across 15 amp threads
releasenotes
Generate formatted changelogs from git history since the last release tag. Use when preparing release notes that categorize changes into breaking changes, features, fixes, and other sections.
relegant
Cross-domain theory connecting Sprague-Grundy computation, graph coloring, Möbius inversion, string diagram composition, and nimber arithmetic through incidence algebras
render-deploy
Deploy applications to Render by analyzing codebases, generating render.yaml Blueprints, and providing Dashboard deeplinks. Use when the user wants to deploy, host, publish, or set up their application on Render's cloud platform.
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 Search 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.
restricted-bigquery-dbt-environment
Safe dbt development against BigQuery using test schema isolation. Prevents accidental production writes. Triggers: dbt, bigquery, test schema, production safety.
rf-signal-analysis
Analyze wireless and radio frequency security in applications, protocols, and hardware. Covers WiFi, Bluetooth/BLE, RFID/NFC, Zigbee, LoRa, cellular, and SDR-based analysis. Use when auditing IoT devices, wireless protocols, access control systems, or any RF-enabled infrastructure.
right-adjoint
Right adjoints preserve limits. RAPL.
s
World S Skill
safe-rewriting-advisor
Strategic selective edge removal maintaining spectral gap ≥ 0.25.
say-ukrainian
Non-Ukrainian voices speak Ukrainian via macOS say command. Load when voicing Ukrainian text through foreign TTS voices for counterfactual narration or ostranення effect.
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.
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 smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. 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
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), 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.
screenshot
Use when the user explicitly asks for a desktop or system screenshot (full screen, specific app or window, or a pixel region), or when tool-specific capture capabilities are unavailable and an OS-level capture is needed.
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.
sdf
Software Design for Flexibility: Sussman & Hanson's additive programming, combinators, propagators, and generic dispatch for evolvable systems
seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
second-opinion
Runs external LLM code reviews (OpenAI Codex or Google Gemini CLI) on uncommitted changes, branch diffs, or specific commits. Use when the user asks for a second opinion, external review, codex review, gemini review, or mentions /second-opinion.
security-best-practices
Perform language and framework specific security best-practice reviews and suggest improvements. Trigger only when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go). Do not trigger for general code review, debugging, or non-security tasks.
security-ownership-map
Analyze git repositories to build a security ownership topology (people-to-file), compute bus factor and sensitive-code ownership, and export CSV/JSON for graph databases and visualization. Trigger only when the user explicitly wants a security-oriented ownership or bus-factor analysis grounded in git history (for example: orphaned sensitive code, security maintainers, CODEOWNERS reality checks for risk, sensitive hotspots, or ownership clusters). Do not trigger for general maintainer lists or non-security ownership questions.
security-review
Scan code changes for security vulnerabilities using STRIDE threat modeling, validate findings for exploitability, and output structured results for downstream patch generation. Supports PR review, scheduled scans, and full repository audits.
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