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.
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.
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.
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.
reportlab
PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.
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-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.
shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
stable-baselines3
Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), creating custom Gym environments, implementing callbacks for monitoring and control, using vectorized environments for parallel training, and integrating with deep RL workflows. This skill should be used when users request RL algorithm implementation, agent training, environment design, or RL experimentation.
statistical-analysis
Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.
statsmodels
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
sympy
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
tooluniverse
Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
torchdrug
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.
transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
vaex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory.
zarr-python
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
Claudeisms Operational Guidelines
Apply strict operational protocols for AI task execution including sequential processing, minimal responses, no destructive operations without confirmation
claudisms
Claude Code plugin enforcing operational guidelines, terse responses, sequential execution, and no destructive operations without confirmation.
clojure-review
Review Clojure and ClojureScript code changes for compliance with Metabase coding standards, style violations, and code quality issues. Use when reviewing pull requests or diffs containing Clojure/ClojureScript code.
clojure-write
Guide Clojure and ClojureScript development using REPL-driven workflow, coding conventions, and best practices. Use when writing, developing, or refactoring Clojure/ClojureScript code.
cloudbase-document-database-web-sdk
Use CloudBase document database Web SDK to query, create, update, and delete data. Supports complex queries, pagination, aggregation, and geolocation queries.
Cloudflare Manager
Comprehensive Cloudflare account management for deploying Workers, KV Storage, R2, Pages, DNS, and Routes. Use when deploying cloudflare services, managing worker containers, configuring KV/R2 storage, or setting up DNS/routing. Requires CLOUDFLARE_API_KEY in .env and Bun runtime with dependencies installed.
code-review-excellence
Master effective code review practices to provide constructive feedback, catch bugs early, and foster knowledge sharing while maintaining team morale. Use when reviewing pull requests, establishing review standards, or mentoring developers.
codex-skill
Use when user asks to leverage codex, gpt-5, or gpt-5.1 to implement something (usually implement a plan or feature designed by Claude). Provides non-interactive automation mode for hands-off task execution without approval prompts.
codex
Execute Codex CLI for code analysis, refactoring, and automated code changes. Use when you need to delegate complex code tasks to Codex AI with file references (@syntax) and structured output.
Command Development
This skill should be used when the user asks to "create a slash command", "add a command", "write a custom command", "define command arguments", "use command frontmatter", "organize commands", "create command with file references", "interactive command", "use AskUserQuestion in command", or needs guidance on slash command structure, YAML frontmatter fields, dynamic arguments, bash execution in commands, user interaction patterns, or command development best practices for Claude Code.
Plugin Structure
This skill should be used when the user asks to "create a plugin", "scaffold a plugin", "understand plugin structure", "organize plugin components", "set up plugin.json", "use ${CLAUDE_PLUGIN_ROOT}", "add commands/agents/skills/hooks", "configure auto-discovery", or needs guidance on plugin directory layout, manifest configuration, component organization, file naming conventions, or Claude Code plugin architecture best practices.
competitive-ads-extractor
Extracts and analyzes competitors' ads from ad libraries (Facebook, LinkedIn, etc.) to understand what messaging, problems, and creative approaches are working. Helps inspire and improve your own ad campaigns.
compliance-architecture
Enterprise-grade compliance architecture for SOC 2, HIPAA, GDPR, PCI-DSS. Provides compliance checklists, security controls, audit guidance, and regulatory requirements for serverless and cloud architectures. Activates for compliance, HIPAA, SOC2, SOC 2, GDPR, PCI-DSS, PCI DSS, regulatory, healthcare data, payment card, data protection, audit, security standards, regulated industry, BAA, business associate agreement, DPIA, data protection impact assessment.
component-guidelines-docs
Generate comprehensive component guideline documentation for SEED Design System. Use when creating or updating design guideline documentation in ./docs/content/docs/components directory. This skill helps create high-quality documentation similar to action-button.mdx.
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