foryourhealth111-pixel
340 verified skills571,315 total stars
yeet
Use only when the user explicitly asks to stage, commit, push, and open a GitHub pull request in one flow using the GitHub CLI (`gh`).
tools2,438
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 do not fit in memory.
development2,438
webthinker-deep-research
Deep web research for VCO: multi-hop search+browse+extract with an auditable action trace and a structured report (WebThinker-style).
development2,438
venue-templates
Use when preparing manuscripts, conference papers, or academic posters that need venue-specific templates, LaTeX style files, author guidelines, page limits, anonymity rules, camera-ready formatting, or submission compliance checks.
development2,438
verification-before-completion
Completion-evidence route used before claiming work is complete, fixed, passing, committed, or PR-ready. Requires fresh verification output before success claims. Do not use for root-cause debugging, TDD implementation, test-report packaging, or review-feedback triage.
development2,438
vibe
Vibe Code Orchestrator (VCO) is a governed runtime entry that freezes requirements, bounds execution, and enforces verification and phase cleanup.
development2,438
vercel-deploy
Deploy applications and websites to Vercel. Use when the user requests deployment actions like "deploy my app", "deploy and give me the link", "push this live", or "create a preview deployment".
development2,438
visualization-best-practices
Review chart choice, labeling, accessibility, and storytelling quality for existing visualizations. Use as an explicit/manual helper for critique and cleanup, not as the main owner for scientific figure production or general chart generation.
tools2,438
xan
High-performance CSV processing with xan CLI for large tabular datasets, streaming transformations, and low-memory pipelines.
tools2,438
vscode-release-notes-writer
Guidelines for writing and reviewing Insiders and Stable release notes for Visual Studio Code.
development2,438
video-studio
Use when the user asks to create or edit videos end-to-end (script→video, auto-cut/jumpcut, captions/subtitles, polishing for Shorts/Reels/TikTok). Current implemented backend: local FFmpeg (probe/render/jumpcut/burn-subtitles/polish). Planned/optional backends: Remotion (motion graphics templates), VectCutAPI (CapCut/剪映 timeline editing), and video-audio-mcp (MCP tool wrapper) when available. Produces a finished video artifact (MP4 by default) from assets + copy + a design/storyboard plan.
tools2,438
windows-hook-debugging
Windows环境下Claude Code插件Hook执行错误的诊断与修复。当遇到hook error、cannot execute binary file、.sh regex误匹配、WSL/Git Bash冲突时使用。
development2,438
writing-plans
Use when you have a spec or requirements for a multi-step task, before touching code
development2,438
Verification & Quality Assurance
Comprehensive truth scoring, code quality verification, and automatic rollback system with 0.95 accuracy threshold for ensuring high-quality agent outputs and codebase reliability.
development2,438
uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
development2,438
weights-and-biases
Track ML experiments with automatic logging, visualize training in real-time, optimize hyperparameters with sweeps, and manage model registry with W&B - collaborative MLOps platform
data-ai2,438
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.
development2,438
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
tools2,438
writing-docs
Guides for writing and editing Remotion documentation. Use when adding docs pages, editing MDX files in packages/docs, or writing documentation content.
documentation2,438
ux-researcher-designer
UX research and design toolkit for Senior UX Designer/Researcher including data-driven persona generation, journey mapping, usability testing frameworks, and research synthesis. Use for user research, persona creation, journey mapping, and design validation.
tools2,438
tensorboard
Visualize training metrics, debug models with histograms, compare experiments, visualize model graphs, and profile performance with TensorBoard - Google's ML visualization toolkit
tools2,398
timesfm-forecasting
Zero-shot time series forecasting with Google's TimesFM foundation model. Use this skill when forecasting ANY univariate time series — sales, sensor readings, stock prices, energy demand, patient vitals, weather, or scientific measurements — without training a custom model. Automatically checks system RAM/GPU before loading the model, supports CSV/DataFrame/array inputs, and returns point forecasts with calibrated prediction intervals. Includes a preflight system checker script that MUST be run before first use to verify the machine can load the model. For classical statistical time series models (ARIMA, SARIMAX, VAR) use statsmodels; for time series classification/clustering use aeon.
development2,398
stable-baselines3
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.
development2,398
usfiscaldata
Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or any U.S. government financial statistics.
development2,398
transcribe
Transcribe audio files to text with optional diarization and known-speaker hints. Use when a user asks to transcribe speech from audio/video, extract text from recordings, or label speakers in interviews or meetings.
content-media2,398
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.
data-ai2,398
think-harder
4-phase structured analysis wrapper for vibe pre-routing (compatible with claude-code-settings think-harder semantics).
development2,398
theme-factory
Toolkit for styling artifacts with a theme. These artifacts can be slides, docs, reportings, HTML landing pages, etc. There are 10 pre-set themes with colors/fonts that you can apply to any artifact that has been creating, or can generate a new theme on-the-fly.
tools2,398
spreadsheet
Use when tasks involve creating, editing, analyzing, or formatting spreadsheets (`.xlsx`, `.csv`, `.tsv`) using Python (`openpyxl`, `pandas`), especially when formulas, references, and formatting need to be preserved and verified.
development2,398
structured-content-storage
Enforces structured, highly documented storage for code and data projects. Use when working on machine learning scripts, data processing, code creation, or script modification that should preserve clear structure and documentation.
development2,398
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.
tools2,398
statsmodels
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
tools2,398
treatment-plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
tools2,398
umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
data-ai2,398
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For broader biological evidence lookup across databases, use bio-database-evidence. Use this for direct HTTP/REST work or UniProt-specific control.
development2,398
submission-checklist
Stage-based submission checklists for papers/reports: pre-submission, submission, revision/rebuttal, camera-ready. Includes templates (cover letter, rebuttal matrix) and quality gates.
testing2,398
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.
tools2,398
tdd-guide
Test-first development route for TDD, writing failing tests first, RED -> GREEN -> REFACTOR, and behavior-changing feature/bug/refactor work. Do not use for already-failing test root-cause debugging, test-report packaging, or final completion evidence.
development2,398
systematic-debugging
Root-cause route for actual bugs, failing tests, build errors, crashes, stack traces, and unexpected behavior. Do not use for test-first/TDD feature work, test-report packaging, review-feedback handling, or final completion evidence.
development2,398
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.
development2,398
subagent-driven-development
Use when executing implementation plans with independent tasks in the current session
development2,398
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
tools2,398
statistics-math
Statistics, probability, linear algebra, and mathematical foundations for data science
testing2,398
unsloth
Expert guidance for fast fine-tuning with Unsloth - 2-5x faster training, 50-80% less memory, LoRA/QLoRA optimization
data-ai2,398
transformer-lens-interpretability
Provides guidance for mechanistic interpretability research using TransformerLens to inspect and manipulate transformer internals via HookPoints and activation caching. Use when reverse-engineering model algorithms, studying attention patterns, or performing activation patching experiments.
development2,398
tiledbvcf
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
testing2,398
hypothesis-generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Also owns explicit HypoGeniC-style or automated LLM-driven hypothesis generation/testing requests inside this single skill. For open-ended ideation use scientific-brainstorming.
testing2,393
paper-2-web
Use when converting academic papers into dissemination assets such as Paper2Web websites, Paper2Video video abstracts, or Paper2Poster conference posters from LaTeX or PDF sources.
development2,393
figma-implement-design
Translate Figma nodes into production-ready code with 1:1 visual fidelity using the Figma MCP workflow (design context, screenshots, assets, and project-convention translation). Trigger when the user provides Figma URLs or node IDs, or asks to implement designs or components that must match Figma specs. Requires a working Figma MCP server connection.
tools2,393
fluidsim
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
development2,393
speech
Use when the user asks for text-to-speech narration or voiceover, accessibility reads, audio prompts, or batch speech generation via the OpenAI Audio API; run the bundled CLI (`scripts/text_to_speech.py`) with built-in voices and require `OPENAI_API_KEY` for live calls. Custom voice creation is out of scope.
tools2,393
speckit-implement
Execute all tasks from the task breakdown to build the feature. Use after task generation to systematically implement the planned solution following TDD approach where applicable.
development2,393
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
development2,393
speckit-plan
Generate technical implementation plans from feature specifications. Use after creating a spec to define architecture, tech stack, and implementation phases. Creates plan.md with detailed technical design.
testing2,393
scholarly-publishing
Use when planning an end-to-end scholarly publishing workflow, including manuscript source-of-truth, submission assets, revision/rebuttal files, camera-ready checks, reproducible build expectations, and publication package structure.
development2,393
similarity-search-patterns
Implement efficient similarity search with vector databases. Use when building semantic search, implementing nearest neighbor queries, or optimizing retrieval performance.
development2,393
speckit-tasks
Break down implementation plans into actionable task lists. Use after planning to create a structured task breakdown. Generates tasks.md with ordered, dependency-aware tasks.
tools2,393
splitting-datasets
Split datasets into training, validation, and test partitions with the right stratification and temporal rules. Use as a narrow preprocessing helper once the broader ML workflow is already chosen, not as the main route owner for an end-to-end ML task.
tools2,393
preprocessing-data-with-automated-pipelines
Design and implement repeatable preprocessing pipelines for cleaning, encoding, transforming, and validating ML input data.
devops2,393
performing-causal-analysis
Estimate causal effects from existing data. Use when fitting or interpreting DiD, ITS, synthetic control, regression discontinuity, or other treatment-effect analyses, including robustness checks and counterfactual plots. For choosing a study design before analysis, use designing-experiments instead.
testing2,393
matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
development2,393
metric-calculator
Compute well-defined metrics from existing formulas, datasets, or test outputs. Use as an explicit/manual helper when the metric definition is already known, not for choosing the overall analysis owner or dashboard strategy.
tools2,393
latex-submission-pipeline
Use when building a LaTeX manuscript submission pipeline with templates, latexmk, BibTeX/Biber, chktex, latexindent, CI PDF builds, compile debugging, and submission zip packaging.
development2,393
creating-data-visualizations
Create analytical charts and plots from existing data. Use for exploratory or reporting visuals such as bars, lines, scatters, and dashboards; not for publication-grade scientific figures or AI-generated schematics.
testing2,393
market-research-reports
Generate comprehensive market research reports and industry/competitive analysis in the style of top consulting firms. Use for market sizing, competitive landscape, market entry, investment thesis, strategic recommendations, and consulting-style business reports. Do not use for scientific reports, paper writing, LaTeX submission/PDF builds, EDGAR/FRED/Treasury/Data Commons data retrieval, or biomedical literature evidence work.
development2,393
pydicom
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
development2,393
latex-posters
Use when creating or revising LaTeX research posters with beamerposter, tikzposter, or baposter, including poster layout, typography, color, print sizing, figure placement, QR codes, compilation, and print-ready PDF checks.
development2,393
knowledge-steward
AI工作经验知识库管理。适用于用户明确要求'保存到Obsidian'、'记录这个'、'save this insight'、'memo this'、'capture this'等知识沉淀场景。将对话中的提示词、模式、问题修复、想法和效率优化保存到Obsidian知识库，并自动同步到GitHub。
data-ai2,393
autonomous-builder
Full-stack software development agent for design, implementation, testing, and deployment. Use when the user explicitly asks for end-to-end project creation, feature development, bug fixing, or code refactoring.
development2,393
bio-database-evidence
Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, target-disease evidence, protein structures, protein interaction networks, reference single-cell census queries, and cross-database biological ID mapping. Do not use for full single-cell analysis, bulk RNA-seq differential expression, BAM/VCF processing, protein embedding models, metabolic flux modeling, genomic interval ML, or flow-cytometry file parsing.
tools2,393
evaluating-machine-learning-models
Evaluate trained machine learning models with the right metrics and comparison logic. Use for benchmark review, threshold selection, calibration, validation, and model comparison; not for feature engineering or leakage auditing.
testing2,393
biopython
Primary retained Python toolkit for molecular biology sequence work. Preferred for sequence manipulation, FASTA/FASTQ/GenBank parsing, Bio.Entrez, BLAST workflows, alignments, structures, and phylogenetics. For biological database evidence lookup, use bio-database-evidence. For single-cell workflows use scanpy. For direct literature REST API, use pubmed-database.
tools2,393
designing-experiments
Design experiments and quasi-experiments before analysis. Use when choosing study design, treatment/control structure, outcomes, assumptions, validation plans after scientific experiment failure, or which of DiD, ITS, synthetic control, or regression discontinuity fits the research question. For fitting models or estimating effects on existing data, use performing-causal-analysis instead.
testing2,393
datacommons-client
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
tools2,393
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
development2,393
citation-management
Comprehensive citation management for academic research. Resolve bibliographic identifiers, extract accurate metadata, validate citations, deduplicate references, and generate properly formatted BibTeX entries. This skill should be used when you need to verify citation information, convert DOIs/PMIDs/arXiv IDs to BibTeX, or ensure reference accuracy in scientific writing.
development2,393
claude-skills
Claude Skills meta-skill: extract domain material (docs/APIs/code/specs) into a reusable Skill (SKILL.md + references/scripts/assets), and refactor existing Skills for clarity, activation reliability, and quality gates.
development2,393
speckit-taskstoissues
Convert tasks from tasks.md into GitHub issues. Use after task breakdown to track work items in GitHub project management.
tools2,393
speckit-constitution
Create or update project governing principles and development guidelines. Use at project start to establish code quality, testing standards, and architectural constraints that guide all development.
development2,393
Error Resolver
Legacy error-resolution reference archive retained for migration. Do not route user tasks here; use systematic-debugging for active bug, stack-trace, and root-cause work.
development2,393
commit-with-reflection
Git提交与调试反思报告生成技能。用于分析开发过程中的错误、调试步骤和解决方案,生成结构化的中文反思报告,并创建包含报告引用的Git提交。显式请求词:反思提交、智能提交、生成调试报告、commit with reflection。
tools2,393
detecting-data-anomalies
Investigate outliers, rare events, spikes, and suspicious records in datasets. Use as an explicit anomaly-analysis helper when you want concrete anomaly-detection workflow guidance, not generic data validation or end-to-end ML ownership.
tools2,393
code-reviewer
Default code-quality route for broad code review, PR review, maintainability, correctness, and regression-risk checks. Do not use as the primary route for dedicated OWASP/security audits, review-feedback handling, completion verification, AI-code cleanup, or TDD/test-first work.
development2,393
sparse-autoencoder-training
Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.
development2,393
spec-kit-vibe-compat
Compatibility router for /speckit.* workflows into /vibe-first Codex execution.
development2,393
skypilot-multi-cloud-orchestration
Multi-cloud orchestration for ML workloads with automatic cost optimization. Use when you need to run training or batch jobs across multiple clouds, leverage spot instances with auto-recovery, or optimize GPU costs across providers.
devops2,393
skill-lookup
Activates when the user asks about Agent Skills, wants to find reusable AI capabilities, needs to install skills, or mentions skills for Claude. Use for discovering, retrieving, and installing skills.
data-ai2,393
bundled/skills/deslop
--- name: deslop description: Remove AI-generated code slop from a branch: unnecessary comments, redundant defensive checks, boilerplate, style drift, and type casts. Use for cleanup of AI-written code, not for broad code review, security audit, TDD, or final verification. --- # Remove AI Code Slop Check the diff against main and remove all AI-generated slop introduced in this branch. ## Routing Boundary Use this skill when the user's problem is cleanup of AI-generated code noise. If the use
development2,393
explaining-machine-learning-models
Explain trained machine learning models through feature attribution, local explanations, and behavior summaries. Use as an explicit/manual helper once a model already exists, not for training ownership, leakage auditing, or general ML strategy selection.
tools2,393
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.
development2,393
matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
development2,393
documentation-lookup
Use when the user needs current library, framework, or API documentation and version-specific code examples.
development2,393
speckit-specify
Create or update feature specifications from natural language descriptions. Use when starting new features or refining requirements. Generates spec.md with user stories, functional requirements, and acceptance criteria following spec-driven development methodology.
development2,393
speckit-clarify
Structured clarification workflow for underspecified requirements. Use before planning to resolve ambiguities through coverage-based questioning. Records answers in spec clarifications section.
testing2,393
speckit-checklist
Generate custom quality checklists for validating requirements completeness and clarity. Use to create unit tests for English that ensure spec quality before implementation.
testing2,393
scanpy
Single-cell RNA-seq and retained scverse workflow owner. Load .h5ad/10X data, manage AnnData metadata, plan scVI/scANVI batch-correction workflows, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
data-ai2,393
security-reviewer
Dedicated security-audit route for OWASP-style risks, secret leaks, auth flaws, injection, unsafe input handling, SSRF/XSS, and sensitive-data exposure. Use instead of code-reviewer when the prompt explicitly asks for security, vulnerability, threat, auth, or OWASP review.
development2,393
neuropixels-analysis
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
testing2,393
speckit-analyze
Perform cross-artifact consistency analysis across spec.md, plan.md, and tasks.md. Use after task generation to identify gaps, duplications, and inconsistencies before implementation.
testing2,393
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.
development2,393
smart-file-writer
Intelligent file write error handler: diagnoses permissions, disk space, path length, file locks before retrying. Use when you encounter 'Error writing file', 'Permission denied', 'Access denied', 'No space left', or related file write failures.
documentation2,393
scientific-writing
Use when writing or revising scientific manuscript prose: IMRAD sections, abstracts, figure/table captions, citation-integrated paragraphs, reporting-guideline language, terminology, clarity, and journal-submission text.
testing2,393
skill-creator
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.
tools2,393
scientific-brainstorming
Open-ended scientific ideation partner. Use for research gaps, mechanism exploration, interdisciplinary connections, assumptions, possible research directions, and lightweight literature matrix or A+B paper-combination idea mapping. For structured testable hypotheses and validation plans, use hypothesis-generation instead.
testing2,393
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.
development2,393
slides-as-code
Build research slides with text-first source (Slidev/Marp/Reveal/Quarto) and reproducible export (PDF). Includes structure, figure reuse rules, and quality checklist for top-tier scientific presentations.
development2,393
research-grants
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
development2,393
pathml
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
tools2,393
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
development2,393
histolab
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
devops2,393
requesting-code-review
Prepare and request a code review after implementation or before merge by assembling scope, requirements, git range, and reviewer instructions.
development2,393
receiving-code-review
Review-feedback handling route for CodeRabbit, GitHub, PR, or human reviewer comments. Use before implementing suggestions to verify each finding. Do not use for a fresh code review, security audit, TDD, or final completion evidence.
development2,393
pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
development2,393
pymc-bayesian-modeling
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
development2,393
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
testing2,393
rdkit
Core cheminformatics toolkit for SMILES/SDF/InChI parsing, descriptors (MW, LogP, TPSA), fingerprints, ECFP/Morgan fingerprints, substructure search, 2D/3D generation, similarity, reactions, and datamol-style molecule standardization when no separate wrapper skill is routed.
tools2,393
scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
development1,760
reviewing-code
Compatibility alias for legacy reviewing-code routes. Delegate to the canonical local `code-reviewer` payload while preserving route compatibility.
development1,760
security-threat-model
Repository-grounded threat modeling that enumerates trust boundaries, assets, attacker capabilities, abuse paths, and mitigations, and writes a concise Markdown threat model. Trigger only when the user explicitly asks to threat model a codebase or path, enumerate threats/abuse paths, or perform AppSec threat modeling. Do not trigger for general architecture summaries, code review, or non-security design work.
development1,760
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.
development1,760
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.
development1,760
senior-prompt-engineer
World-class prompt engineering skill for LLM optimization, prompt patterns, structured outputs, and AI product development. Expertise in Claude, GPT-4, prompt design patterns, few-shot learning, chain-of-thought, and AI evaluation. Includes RAG optimization, agent design, and LLM system architecture. Use when building AI products, optimizing LLM performance, designing agentic systems, or implementing advanced prompting techniques.
development1,760
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.
development1,760
scholar-evaluation
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
development1,760
scientific-reporting
Write research/technical reports with strong structure + figure standards. Supports Markdown/HTML/PDF outputs (Quarto optional), executive summary, methods, results, discussion, and reproducibility appendix.
development1,760
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.
testing1,760
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.
development1,760
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.
tools1,760
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.
development1,760
running-clustering-algorithms
Segment data with clustering algorithms such as K-means, DBSCAN, or hierarchical clustering. Use for unsupervised grouping and cluster diagnostics, not supervised classification or publication-figure ownership.
development1,760
scrapling
CLI-first web scraping & content extraction with optional MCP server. Use when you have target URLs and need clean, selector-based outputs (html/md/txt).
tools1,760
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.
tools1,760
seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
data-ai1,760
sentry
Use when the user asks to inspect Sentry issues or events, summarize recent production errors, or pull basic Sentry health data via the Sentry API; perform read-only queries with the bundled script and require `SENTRY_AUTH_TOKEN`.
development1,760
senior-ml-engineer
World-class ML engineering skill for productionizing ML models, MLOps, and building scalable ML systems. Expertise in PyTorch, TensorFlow, model deployment, feature stores, model monitoring, and ML infrastructure. Includes LLM integration, fine-tuning, RAG systems, and agentic AI. Use when deploying ML models, building ML platforms, implementing MLOps, or integrating LLMs into production systems.
development1,760
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.
tools1,760
scientific-data-preprocessing
⚠️ CRITICAL USER EXPERIENCE-BASED SKILL - ALWAYS CONSULT BEFORE DATA PREPROCESSING ⚠️ Prevents catastrophic errors (88.9% error rate in V1.0 case study) through multi-level feature analysis, data leakage detection, and semantic validation. MANDATORY for: data preprocessing, feature engineering, standardization, normalization, interpolation, missing value handling, feature selection, or ANY data transformation task. Covers grouped time-series, cross-sectional, panel data. Detects: time travel leakage, causal inversion, ID misuse, semantic-numeric fallacies, distribution blindness. User's hard-won lessons from real project failures.
development1,760
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.
tools1,760
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.
testing1,760
engineering-features-for-machine-learning
Create, encode, transform, and select features before model fitting. Use when the user needs feature engineering decisions or implementation, not final training ownership or leakage auditing.
development1,692
report-generator
高级报告生成专家，支持多格式输出、数据可视化和交互式报告生成。
business1,692
feature-importance-analyzer
Explain which features drive a trained model's predictions. Use after a model exists and you need ranking, pruning, or interpretation; not for raw feature engineering or leakage checking.
testing1,692
generating-test-reports
Generate structured test reports with pass/fail rollups, coverage summaries, and test artifacts. Use when the user is asking for test-result packaging or delivery, not for root-cause debugging or feature implementation.
development1,692
ml-data-leakage-guard
Detects and prevents data leakage in machine learning and mathematical modeling. Use after ML tasks involving data cleaning, feature engineering, data augmentation, algorithm development, normalization, missing value imputation, dimensionality reduction, feature selection, or time series modeling. Checks if features/statistics would be available at prediction time.
development1,692
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.
development1,692
regression-analysis-helper
Build and diagnose regression analyses for continuous targets or effect estimation. Use for coefficient interpretation, residual checks, and model comparison; not for causal identification or clustering.
tools1,692
Use when tasks involve reading, creating, or reviewing PDF files where rendering and layout matter; prefer visual checks by rendering pages (Poppler) and use Python tools such as `reportlab`, `pdfplumber`, and `pypdf` for generation and extraction.
tools1,692
providing-performance-optimization-advice
Produce a prioritized performance-optimization roadmap across frontend, backend, and infrastructure. Use as an explicit/manual helper after bottlenecks are known or suspected, not as the owner of regression detection, profiling capture, or test execution.
tools1,692
performing-regression-analysis
Build and diagnose regression models when the main question is regression itself. Use for model specification, coefficient interpretation, residual checks, and fit diagnostics; not for causal identification, generic feature screening, or report packaging.
development1,692
planning-with-files
Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md. Use when starting complex multi-step tasks, research projects, or any task requiring >5 tool calls.
tools1,692
LQF_Machine_Learning_Expert_Guide
LQF Machine Learning Expert Guide - Routed skill for ML/Statistical Modeling with Critical Discussion Mode. Triggers on: machine learning, modeling, prediction, training, classification, regression, clustering, deep learning, neural network, model evaluation, feature engineering, hyperparameter tuning, overfitting, underfitting, baseline, ablation study, critique my approach, review my model, is this a good idea, should I use, what's wrong with, evaluate my solution, challenge my assumptions, discuss my approach Engages in critical discussion with minimum 3 rounds of iterative refinement. Challenges both user proposals and own suggestions with fact-based critique. Demands evidence and baselines before accepting solutions.
development1,603
anomaly-detector
Detect outliers, spikes, rare events, and abnormal records in tabular or time-series data. Use when the task is anomaly detection or suspicious-pattern review, not generic data-quality linting or full ML pipeline ownership.
development1,603
confusion-matrix-generator
Inspect classifier errors with confusion matrices after predictions already exist. Use for per-class error analysis, threshold tradeoffs, and label-confusion diagnosis; not for regression metrics or full model training ownership.
data-ai1,603
data-normalization-tool
Scale and normalize numeric features for model-ready pipelines. Use for z-score, min-max, robust scaling, and train-only statistic handling; not for leakage audits or broader feature-engineering ownership.
tools1,603
data-quality-checker
Validate dataset completeness and basic correctness before downstream analysis. Use for nulls, duplicates, schema drift, range checks, and column-level sanity reviews; not for anomaly detection or ML evaluation.
testing1,603
detecting-performance-regressions
Compare current benchmark results against historical baselines to spot performance regressions. Use as an explicit/manual helper for build-to-build degradation review, not for broad optimization strategy or low-level profiling ownership.
tools1,603
correlation-analyzer
Screen pairwise relationships, collinearity, and simple associations in tabular data. Use when the goal is correlation review or feature screening, not causal claims or final regression modeling.
development1,603
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
development1,422
jupyter-notebook
Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.
tools1,422
openai-docs
Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations (for example: Codex, Responses API, Chat Completions, Apps SDK, Agents SDK, Realtime, model capabilities or limits); prioritize OpenAI docs MCP tools and restrict any fallback browsing to official OpenAI domains.
tools1,422
labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
development1,422
node-zombie-guardian
Use when diagnosing stale or orphaned Node.js processes launched by VCO, auditing ownership/liveness, or safely simulating cleanup without touching external Node workloads.
testing1,422
nowait-reasoning-optimizer
Implements the NOWAIT technique for efficient reasoning in R1-style LLMs. Use when optimizing inference of reasoning models (QwQ, DeepSeek-R1, Phi4-Reasoning, Qwen3, Kimi-VL, QvQ), reducing chain-of-thought token usage by 27-51% while preserving accuracy. Triggers on "optimize reasoning", "reduce thinking tokens", "efficient inference", "suppress reflection tokens", or when working with verbose CoT outputs.
testing1,422
open-notebook
Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports 16+ AI providers including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral with complete data privacy through self-hosting.
development1,422
openalex-database
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.
testing1,422
prowler-docs
Prowler documentation style guide and writing standards. Trigger: When writing documentation for Prowler features, tutorials, or guides.
documentation1,422
performance-testing
Benchmark indicator performance with BenchmarkDotNet. Use for Series/Buffer/Stream benchmarks, regression detection, and optimization patterns. Target 1.5x Series for StreamHub, 1.2x for BufferList.
testing1,422
polars
Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.
development1,422
pubmed-database
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
development1,422
ralph-loop
Codex-compatible Ralph loop runner with dual engines (compat local state loop + optional open-ralph-wiggum backend).
development1,422
document-skills
Umbrella skill for document workflows (PDF/DOCX/XLSX/PPTX). Dispatches to the most specific document skill to reduce noise and improve routing precision.
testing1,422
pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
tools1,422
propositional-logic
Problem-solving strategies for propositional logic in mathematical logic
tools1,422
pylabrobot
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
tools1,422
pyzotero
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
tools1,422
pyhealth
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
tools1,422
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
development1,422
pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
testing1,422
neurokit2
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
tools1,422
medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
development1,422
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
development1,422
qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
development1,422
qiskit
IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
tools1,422
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.
development1,422
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
testing1,422
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.
tools1,422
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.
development1,422
pufferlib
This skill should be used when working with reinforcement learning tasks including high-performance RL training, custom environment development, vectorized parallel simulation, multi-agent systems, or integration with existing RL environments (Gymnasium, PettingZoo, Atari, Procgen, etc.). Use this skill for implementing PPO training, creating PufferEnv environments, optimizing RL performance, or developing policies with CNNs/LSTMs.
development1,422
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
development1,422
prompt-lookup
Activates when the user asks about AI prompts, needs prompt templates, wants to search for prompts, or mentions prompts.chat. Use for discovering, retrieving, and improving prompts.
data-ai1,422
protocolsio-integration
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
development1,422
pptx-posters
Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
development1,422
plotly
Interactive scientific and statistical data visualization library for Python. Use when creating charts, plots, or visualizations including scatter plots, line charts, bar charts, heatmaps, 3D plots, geographic maps, statistical distributions, financial charts, and dashboards. Supports both quick visualizations (Plotly Express) and fine-grained customization (graph objects). Outputs interactive HTML or static images (PNG, PDF, SVG).
development1,422
peer-review
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
development1,422
opentrons-integration
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
tools1,422
opentargets-database
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
testing1,422
openai-knowledge
Compatibility alias for OpenAI platform documentation guidance. Delegate to the canonical local `openai-docs` payload while preserving route compatibility.
documentation1,422
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
tools1,422
modal-labs
Modal Labs (modal.com) — run Python on serverless containers with GPUs, batch jobs, and autoscaling. Precision wrapper to avoid confusion with UI “modal dialogs”.
development1,422
modal
Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
development1,422
ml-pipeline-workflow
Build end-to-end MLOps pipelines from data preparation through model training, validation, and production deployment. Use when creating ML pipelines, implementing MLOps practices, or automating model training and deployment workflows.
development1,422
matplotlib
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
development1,422
math-tools
Deterministic mathematical computation using SymPy. Use for ANY math operation requiring exact/verified results - basic arithmetic, algebra (simplify, expand, factor, solve equations), calculus (derivatives, integrals, limits, series), linear algebra (matrices, determinants, eigenvalues), trigonometry, number theory (primes, GCD/LCM, factorization), and statistics. Ensures mathematical accuracy by using symbolic computation rather than LLM estimation.
tools1,422
markitdown
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
development1,422
markdown-mermaid-writing
Comprehensive markdown and Mermaid diagram writing skill that establishes text-based diagrams as the DEFAULT documentation standard. Use this skill when creating ANY scientific document, report, analysis, or visualization — it ensures all outputs are in version-controlled, token-efficient markdown with embedded Mermaid diagrams as the source of truth, with clear pathways to downstream Python or AI-generated images. Includes full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates ready to use.
development1,422
manuscript-as-code
Treat manuscripts as software: version control, reproducible builds, figure pipelines, CI, and structured repo layout. Helps teams avoid 'final_v7' chaos and ensures submission-ready artifacts.
development1,422
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
development1,422
infographics
Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.
development1,422
hypothesis-testing
Property-based testing with Hypothesis for discovering edge cases and validating invariants. Use when implementing comprehensive test coverage, testing complex logic with many inputs, or validating mathematical properties and invariants across input domains. Triggered by: hypothesis, property-based testing, @given, strategies, generative testing.
testing1,422
hedgefundmonitor
Query the OFR (Office of Financial Research) Hedge Fund Monitor API for hedge fund data including SEC Form PF aggregated statistics, CFTC Traders in Financial Futures, FICC Sponsored Repo volumes, and FRB SCOOS dealer financing terms. Access time series data on hedge fund size, leverage, counterparties, liquidity, complexity, and risk management. No API key or registration required. Use when working with hedge fund data, systemic risk monitoring, financial stability research, hedge fund leverage or leverage ratios, counterparty concentration, Form PF statistics, repo market data, or OFR financial research data.
development1,422
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
tools1,422
ginkgo-cloud-lab
Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.
tools1,422
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
development1,422
cs-foundations
Master discrete mathematics, logic, formal proofs, and computational thinking. Build the mathematical foundation for all computer science.
development1,422
pymc-bayesian-modeling
Compatibility alias for the descriptive PyMC skill name. Delegate to the canonical local `pymc` payload while preserving route and README compatibility.
documentation1,422
pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
tools1,422
property-based-testing
Property-based testing with fast-check (TypeScript/JavaScript) and Hypothesis (Python). Generate test cases automatically, find edge cases, and test mathematical properties. Use when user mentions property-based testing, fast-check, Hypothesis, generating test data, QuickCheck-style testing, or finding edge cases automatically.
development1,422
perplexity-search
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
development1,422
pennylane
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
development1,422
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
data-ai1,422
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
development1,422
MCP Integration
This skill should be used when the user asks to "add MCP server", "integrate MCP", "configure MCP in plugin", "use .mcp.json", "set up Model Context Protocol", "connect external service", mentions "${CLAUDE_PLUGIN_ROOT} with MCP", or discusses MCP server types (SSE, stdio, HTTP, WebSocket). Provides comprehensive guidance for integrating Model Context Protocol servers into Claude Code plugins for external tool and service integration.
tools1,422
mathematical-logic-expert
Expert in formal logic, model theory, computability, and foundations of mathematics
data-ai1,422
math
Unified math capabilities - computation, solving, and explanation. I route to the right tool.
tools1,422
hive-mind-advanced
Advanced Hive Mind collective intelligence system for queen-led multi-agent coordination with consensus mechanisms and persistent memory
data-ai1,422
hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
data-ai1,422
imagegen
Use when the user asks to generate or edit images via the OpenAI Image API (for example: generate image, edit/inpaint/mask, background removal or replacement, transparent background, product shots, concept art, covers, or batch variants); run the bundled CLI (`scripts/image_gen.py`) and require `OPENAI_API_KEY` for live calls.
tools1,422
math-model-selector
Routes problems to appropriate mathematical frameworks using expert heuristics
development1,422
local-vco-roles
Codex-local role pack for dialectic multi-agent reviews, designed to be compatible with the local vibe skill.
development1,422
literature-matrix
Systematic research idea discovery through paper combination matrix. Use when finding research ideas, evaluating paper combinations, building unified theoretical frameworks, or generating code skeletons from combined methods.
development1,422
iso-13485-certification
Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
tools1,422
gh-address-comments
Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.
tools1,422
hypogenic
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
testing1,422
gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
testing1,422
gradient-methods
Problem-solving strategies for gradient methods in optimization
tools1,422
gh-fix-ci
Use when a user asks to debug or fix failing GitHub PR checks that run in GitHub Actions; use `gh` to inspect checks and logs, summarize failure context, draft a fix plan, and implement only after explicit approval. Treat external providers (for example Buildkite) as out of scope and report only the details URL.
development1,422
playwright
Use when the task requires automating a real browser from the terminal (navigation, form filling, snapshots, screenshots, data extraction, UI-flow debugging) via `playwright-cli` or the bundled wrapper script.
tools1,422
netlify-deploy
Deploy web projects to Netlify using the Netlify CLI (`npx netlify`). Use when the user asks to deploy, host, publish, or link a site/repo on Netlify, including preview and production deploys.
tools1,422
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
tools1,051
docx
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks
development1,051
file-organizer
Intelligently organizes your files and folders across your computer by understanding context, finding duplicates, suggesting better structures, and automating cleanup tasks. Reduces cognitive load and keeps your digital workspace tidy without manual effort.
tools1,051
flashrag-evidence
Local evidence retrieval (FlashRAG-style) for VCO/vibe: search protocols/config/skills docs and return citeable snippets with file+line anchors.
testing1,051
evaluating-code-models
Evaluates code generation models across HumanEval, MBPP, MultiPL-E, and 15+ benchmarks with pass@k metrics. Use when benchmarking code models, comparing coding abilities, testing multi-language support, or measuring code generation quality. Industry standard from BigCode Project used by HuggingFace leaderboards.
development1,051
evaluating-llms-harness
Evaluates LLMs across 60+ academic benchmarks (MMLU, HumanEval, GSM8K, TruthfulQA, HellaSwag). Use when benchmarking model quality, comparing models, reporting academic results, or tracking training progress. Industry standard used by EleutherAI, HuggingFace, and major labs. Supports HuggingFace, vLLM, APIs.
development1,051
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
development1,051
G2 Legend Expert
Expert skill for G2 legend development - provides comprehensive knowledge about legend rendering implementation, component architecture, layout algorithms, and interaction handling. Use when implementing, customizing, or debugging legend functionality in G2 visualizations.
development1,051
skill-installer
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
development1,051
skill-creator
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations.
tools1,051
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.
development1,051
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.
development1,051
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
data-ai1,051
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
documentation1,051
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
tools1,051
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
tools1,051
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
development1,051
geomaster
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, and 7 programming languages (Python, R, Julia, JavaScript, C++, Java, Go) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.
development1,051
aios-po
Product Owner (Pax). Use for backlog management, story refinement, acceptance criteria, sprint planning, and prioritization decisions
testing1,051
figma
Use the Figma MCP server to fetch design context, screenshots, variables, and assets from Figma, and to translate Figma nodes into production code. Trigger when a task involves Figma URLs, node IDs, design-to-code implementation, or Figma MCP setup and troubleshooting.
tools1,051
aios-pm
Product Manager (Morgan). Use for PRD creation (greenfield and brownfield), epic creation and management, product strategy and vision, feature prioritization (MoSCoW, RICE), roa...
data-ai1,051
aios-dev
Full Stack Developer (Dex). Use for code implementation, debugging, refactoring, and development best practices
development1,051
aios-qa
Test Architect & Quality Advisor (Quinn). Use for comprehensive test architecture review, quality gate decisions, and code improvement. Provides thorough analysis including requ...
development1,051
aios-squad-creator
Squad Creator (Craft). Use to create, validate, publish and manage squads
testing1,051
aios-ux-design-expert
UX/UI Designer & Design System Architect (Uma). Complete design workflow - user research, wireframes, design systems, token extraction, component building, and quality assurance
development1,051
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.
tools1,051
build-error-resolver
Compatibility alias for build-specific error resolution. Use this when VCO routes to build-error-resolver but the upstream agent is unavailable in the current runtime.
development1,051
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
data-ai1,051
doc
Use when the task involves reading, creating, or editing `.docx` documents, especially when formatting or layout fidelity matters; prefer `python-docx` plus the bundled `scripts/render_docx.py` for visual checks.
development1,051
data-exploration-visualization
自动化数据探索和可视化工具，提供从数据加载到专业报告生成的完整EDA解决方案。支持多种图表类型、智能数据诊断、建模评估和HTML报告生成。适用于医疗、金融、电商等领域的数据分析项目。
development1,051
datavis
Comprehensive data visualization toolkit for creating beautiful, mathematically elegant visualizations with D3.js, Chart.js, and custom SVG. Use when (1) building interactive data visualizations, (2) designing color palettes for charts, (3) choosing scales and visual encodings, (4) creating data pipelines from Census/SEC/Wikipedia APIs, (5) crafting narrative-driven data stories, (6) making perceptually accurate charts, or (7) implementing force-directed networks, timelines, or geographic maps.
tools1,051
deepagent-memory-fold
DeepAgent-style memory folding for VCO sessions: compress long context into structured working/tool memory without using episodic-memory.
tools1,051
deepagent-toolchain-plan
DeepAgent-style tool discovery for VCO: propose a minimal skill/tool chain (with verification points) and reduce confirm_required friction.
tools1,051
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
tools1,051
docx-comment-reply
Reply to comments (批注) in Word .docx/.doc files: extract comment context, draft replies, write threaded replies back, and validate OOXML.
testing1,051
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.
tools1,051
experiment-failure-analysis
Systematically analyze experiment failures and optimization setbacks to identify root causes and define validation plans before abandonment decisions.
testing1,051
flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
data-ai1,051
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
development1,051
aios-analyst
Business Analyst (Atlas). Use for market research, competitive analysis, user research, brainstorming session facilitation, structured ideation workshops, feasibility studies, i...
testing1,051
gget
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
tools1,051
generate-image
Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
testing1,051
Excel Analysis
Analyze Excel spreadsheets, create pivot tables, generate charts, and perform data analysis. Use when analyzing Excel files, spreadsheets, tabular data, or .xlsx files.
data-ai1,051
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
tools1,051
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.
development1,051
deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
testing1,051
debugging-strategies
Master systematic debugging techniques, profiling tools, and root cause analysis to efficiently track down bugs across any codebase or technology stack. Use when investigating bugs, performance issues, or unexpected behavior.
tools1,051
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
development1,051
coding-tutor
Personalized coding tutorials that build on your existing knowledge and use your actual codebase for examples. Creates a persistent learning trail that compounds over time using the power of AI, spaced repetition and quizes.
development1,051
code-review
Code review assistance with linting, style checking, and best practices
development1,051
fred-economic-data
Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring U.S. and international economic indicators.
development1,051
architecture-patterns
Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use when architecting complex backend systems or refactoring existing applications for better maintainability.
development1,051
aios-master
AIOS Master Orchestrator & Framework Developer (Orion). Use when you need comprehensive expertise across all domains, framework component creation/modification, workflow orchest...
development1,051
evals-context
Provides context about the Roo Code evals system structure in this monorepo. Use when tasks mention "evals", "evaluation", "eval runs", "eval exercises", or working with the evals infrastructure. Helps distinguish between the evals execution system (packages/evals, apps/web-evals) and the public website evals display page (apps/web-roo-code/src/app/evals).
development1,051
aios-devops
GitHub Repository Manager & DevOps Specialist (Gage). Use for repository operations, version management, CI/CD, quality gates, and GitHub push operations. ONLY agent authorized...
development1,051
algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
development1,051
alpha-vantage
Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Requires a free API key from alphavantage.co.
development1,051
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.
development1,051
get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
development1,051
geopandas
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
tools1,051
bgpt-paper-search
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.
tools1,051
brainstorming
You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.
development1,051
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.
tools1,051
astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
development1,051
cancel-ralph
Codex-compatible cancel command for Ralph loop state, preserving the original command name.
development1,051
aios-architect
Architect (Aria). Use for system architecture (fullstack, backend, frontend, infrastructure), technology stack selection (technical evaluation), API design (REST/GraphQL/tRPC/We...
development1,051
gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
development1,051
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.
development1,051
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
development1,051
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
tools1,051
dask
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.
data-ai1,051
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
testing1,051
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.
tools1,051
cellxgene-census
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
data-ai1,051
anndata
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
tools1,051
alphafold-database
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
testing1,051
aeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
development1,051
docs-write
Write documentation following Metabase's conversational, clear, and user-focused style. Use when creating or editing documentation files (markdown, MDX, etc.).
documentation1,051
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
tools1,051
aios-sm
Scrum Master (River). Use for user story creation from PRD, story validation and completeness checking, acceptance criteria definition, story refinement, sprint planning, backlo...
testing1,051
dialectic
Minimal compatibility wrapper for vibe Dialectic Mode (multi-perspective design analysis).
content-media1,051
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.
testing1,051
data-artist
Create beautiful data visualizations with mathematical elegance, color theory, and narrative design - the "Data is Beautiful" aesthetic.
data-ai1,051
create-plan
Create a concise plan. Use when a user explicitly asks for a plan related to a coding task.
testing1,051
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
tools1,051
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
development1,051
aios-data-engineer
Database Architect & Operations Engineer (Dara). Use for database design, schema architecture, Supabase configuration, RLS policies, migrations, query optimization, data modelin...
testing1,051
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.
tools1,051
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.
tools1,051
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
development1,051
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.
tools1,051
edgartools
Python library for accessing, analyzing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings.
tools1,051
embedding-strategies
Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.
testing1,051
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.
development1,051
comprehensive-research-agent
Ensure thorough validation, error recovery, and transparent reasoning in research tasks with multiple tool calls
tools1,051
content-research-writer
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section. Transforms your writing process from solo effort to collaborative partnership.
testing1,051
context-fundamentals
This skill should be used when the user asks to "understand context", "explain context windows", "design agent architecture", "debug context issues", "optimize context usage", or discusses context components, attention mechanics, progressive disclosure, or context budgeting. Provides foundational understanding of context engineering for AI agent systems.
development1,051
context-hunter
Discover codebase patterns, conventions, and unwritten rules before making changes. Use when implementing features, fixing bugs, or refactoring code.
development1,051
data-quality-frameworks
Implement data quality validation with Great Expectations, dbt tests, and data contracts. Use when building data quality pipelines, implementing validation rules, or establishing data contracts.
development1,051
data-storytelling
Transform data into compelling narratives using visualization, context, and persuasive structure. Use when presenting analytics to stakeholders, creating data reports, or building executive presentations.
development1,051
digital-brain
This skill should be used when the user asks to "write a post", "check my voice", "look up contact", "prepare for meeting", "weekly review", "track goals", or mentions personal brand, content creation, network management, or voice consistency.
development1,051
docs-review
Review documentation changes for compliance with the Metabase writing style guide. Use when reviewing pull requests, files, or diffs containing documentation markdown files.
documentation1,051