jackspace/claudeskillz

base-ui-react

Production-tested setup for Base UI (@base-ui-components/react) - MUI's unstyled component library that provides accessible, customizable React components using render props pattern. This skill should be used when building accessible UIs with full styling control, migrating from Radix UI, or needing components with Floating UI integration for smart positioning. Use when: Setting up Base UI in Vite + React projects, migrating from Radix UI to Base UI, implementing accessible components (Dialog, Select, Popover, Tooltip, NumberField, Accordion), encountering positioning issues with popups, needing render prop API instead of asChild pattern, building with Tailwind v4 + shadcn/ui, or deploying to Cloudflare Workers. ⚠️ BETA STATUS: Base UI is v1.0.0-beta.4. Stable v1.0 expected Q4 2025. This skill provides workarounds for known beta issues and guidance on API stability. Keywords: base-ui, @base-ui-components/react, mui base ui, unstyled components, accessible components, render props, radix alternative, radix migration, floating-ui, positioner pattern, headless ui, accessible dialog, accessible select, accessible popover, accessible tooltip, accessible accordion, number field, react components, tailwind components, vite react, cloudflare workers ui, beta components, component library

cloudflare-nextjs

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rapid-prototyper

Creates minimal working prototypes for quick idea validation. Single-file when possible, includes test data, ready to demo immediately. Use when user says "prototype", "MVP", "proof of concept", "quick demo".

hugo

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ai-elements-chatbot

This skill provides production-ready AI chat UI components built on shadcn/ui for conversational AI interfaces. Use when building ChatGPT-style chat interfaces with streaming responses, tool/function call displays, reasoning visualization, or source citations. Provides 30+ components including Message, Conversation, Response, CodeBlock, Reasoning, Tool, Actions, Sources optimized for Vercel AI SDK v5. Prevents common setup errors with Next.js App Router, Tailwind v4, shadcn/ui integration, AI SDK v5 migration, component composition patterns, voice input browser compatibility, responsive design issues, and streaming optimization. Keywords: ai-elements, vercel-ai-sdk, shadcn, chatbot, conversational-ai, streaming-ui, chat-interface, ai-chat, message-components, conversation-ui, tool-calling, reasoning-display, source-citations, markdown-streaming, function-calling, ai-responses, prompt-input, code-highlighting, web-preview, branch-navigation, thinking-display, perplexity-style, claude-artifacts

repository-analyzer

Analyzes codebases to generate comprehensive documentation including structure, languages, frameworks, dependencies, design patterns, and technical debt. Use when user says "analyze repository", "understand codebase", "document project", or when exploring unfamiliar code.

better-chatbot-patterns

This skill provides reusable implementation patterns extracted from the better-chatbot project for custom AI chatbot deployments. Use this skill when building AI chatbots with server action validators, tool abstraction systems, workflow execution, or multi-AI provider integration in your own projects (not contributing to better-chatbot itself). Use when: building AI chatbot features, implementing server action validators, creating tool abstraction layers, setting up multi-AI provider support, building workflow execution systems, adapting better-chatbot patterns to custom projects Keywords: AI chatbot patterns, server action validators, tool abstraction, multi-AI providers, workflow execution, MCP integration, validated actions, tool type checking, Vercel AI SDK patterns, chatbot architecture

web-asset-generator

Generate web assets including favicons, app icons (PWA), and social media meta images (Open Graph) for Facebook, Twitter, WhatsApp, and LinkedIn. Use when users need icons, favicons, social sharing images, or Open Graph images from logos or text slogans. Handles image resizing, text-to-image generation, and provides proper HTML meta tags.

multi-repository-orchestrator

Coordinate development workflows across multiple Git repositories with synchronized branching, batch commits, cross-repo operations, and monorepo-like workflows for microservices and multi-package projects.

docker-helper

Expert helper for Docker containers, Docker Compose, and container optimization

cloudflare-full-stack-integration

Production-tested integration patterns for connecting React frontends to Cloudflare Worker backends with Hono, Clerk authentication, and D1 databases. Prevents common frontend-backend connection issues, CORS errors, auth token failures, and race conditions. Use when: connecting frontend to backend, implementing auth flow, setting up API calls, troubleshooting CORS, fixing race conditions, auth tokens not passing, frontend-backend connection errors, 401 errors, integrating Clerk with Workers, setting up full-stack Cloudflare app, vite cloudflare plugin setup. Prevents: CORS errors, 401 Unauthorized, auth token mismatches, race conditions with auth loading, environment variable confusion, frontend calling wrong endpoints, JWT verification errors, D1 connection issues. Keywords: frontend backend integration, Cloudflare Workers, Hono, Clerk auth, JWT verification, CORS, React API client, race conditions, auth loading, connection issues, full-stack integration, vite plugin, @cloudflare/vite-plugin, D1 database, environment variables, token attachment, session management, protected routes, API middleware

cloudflare-zero-trust-access

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devops

Deploy and manage cloud infrastructure on Cloudflare (Workers, R2, D1, KV, Pages, Durable Objects, Browser Rendering), Docker containers, and Google Cloud Platform (Compute Engine, GKE, Cloud Run, App Engine, Cloud Storage). Use when deploying serverless functions to the edge, configuring edge computing solutions, managing Docker containers and images, setting up CI/CD pipelines, optimizing cloud infrastructure costs, implementing global caching strategies, working with cloud databases, or building cloud-native applications.

ui-styling

Create beautiful, accessible user interfaces with shadcn/ui components (built on Radix UI + Tailwind), Tailwind CSS utility-first styling, and canvas-based visual designs. Use when building user interfaces, implementing design systems, creating responsive layouts, adding accessible components (dialogs, dropdowns, forms, tables), customizing themes and colors, implementing dark mode, generating visual designs and posters, or establishing consistent styling patterns across applications.

cloudflare-email-routing

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chrome-devtools

Browser automation, debugging, and performance analysis using Puppeteer CLI scripts. Use for automating browsers, taking screenshots, analyzing performance, monitoring network traffic, web scraping, form automation, and JavaScript debugging.

windows-expert

Expert guidance for Windows, PowerShell, WSL interop, and cross-platform development

exploratory-data-analysis

Analyze datasets to discover patterns, anomalies, and relationships. Use when exploring data files, generating statistical summaries, checking data quality, or creating visualizations. Supports CSV, Excel, JSON, Parquet, and more.

network-diagnostics

Automated network troubleshooting and diagnostics for WSL/Linux environments

tailwind-v4-shadcn

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error-debugger

Analyzes errors, searches past solutions in memory, provides immediate fixes with code examples, and saves solutions for future reference. Use when user says "debug this", "fix this error", "why is this failing", or when error messages appear like TypeError, ECONNREFUSED, CORS, 404, 500, etc.

checkpoint-workflow-builder

Build resumable state-machine workflows with checkpoint patterns, progress preservation, and automatic recovery for complex multi-phase operations that need to survive interruptions, timeouts, and failures.

firecrawl-scraper

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哔哩哔哩字幕获取器

project-session-management

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terraform-iac-helper

Expert helper for Terraform and infrastructure-as-code best practices

zustand-state-management

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timeout-prevention

Prevent request timeouts in Claude Code sessions by chunking long operations, implementing progress checkpoints, using background processes, and optimizing tool usage patterns. Use when performing bulk operations, processing large datasets, running long-running commands, downloading multiple files, or executing tasks that exceed 2-minute timeout limits. Implements strategies like task decomposition, incremental processing, parallel execution, checkpoint-resume patterns, and efficient resource management to ensure reliable completion of complex workflows.

cloudflare-sandbox

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bash-script-helper

Expert helper for bash scripting, debugging, and best practices

claude-git-branching

Expert Git workflow management for Claude Code sessions with branch naming conventions, push retry logic, conflict resolution, and PR automation specifically designed for AI-assisted development workflows.

cloudflare-cron-triggers

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brainstorming

Use when creating or developing anything, before writing code or implementation plans - refines rough ideas into fully-formed designs through structured Socratic questioning, alternative exploration, and incremental validation

yaml-config-helper

Validate, format, and troubleshoot YAML configuration files

cloudflare-agents

Build AI agents on Cloudflare Workers with MCP integration, tool use, and LLM providers.

claude-code-bash-patterns

Claude Code Bash tool patterns with hooks, automation, git workflows. Use for PreToolUse hooks, command chaining, CLI orchestration, custom commands, or encountering bash permissions, command failures, security guards, hook configurations.

project-planning

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github-auth

Securely authenticate with GitHub using stored credentials for API operations and git commands

nextjs

Next.js 16 App Router performance optimization guidelines (formerly nextjs-16-app-router). This skill should be used when writing Next.js 16 code, configuring caching, implementing Server Components in Next.js, setting up App Router routing, or configuring next.config.js. This skill does NOT cover generic React 19 patterns (use react-19 skill) or non-Next.js server rendering.

thesys-generative-ui

AI-powered generative UI with Thesys - create React components from natural language.

auth-js

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better-chatbot

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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.

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.

drizzle-orm-d1

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scholar-evaluation

Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill should be used when assessing research papers, evaluating literature reviews, scoring research methodologies, analyzing scientific writing quality, or applying structured evaluation criteria to academic work. Provides comprehensive assessment across multiple dimensions including problem formulation, literature review, methodology, data collection, analysis, results interpretation, and scholarly writing quality.

git-workflow-helper

Expert guidance for Git workflows, troubleshooting, and best practices

cloudflare-workers-ai

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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).

dispatching-parallel-agents

Use when facing 3+ independent failures that can be investigated without shared state or dependencies - dispatches multiple Claude agents to investigate and fix independent problems concurrently

claude-agent-sdk

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transformers

Work with state-of-the-art machine learning models for NLP, computer vision, audio, and multimodal tasks using HuggingFace Transformers. This skill should be used when fine-tuning pre-trained models, performing inference with pipelines, generating text, training sequence models, or working with BERT, GPT, T5, ViT, and other transformer architectures. Covers model loading, tokenization, training with Trainer API, text generation strategies, and task-specific patterns for classification, NER, QA, summarization, translation, and image tasks. (plugin:scientific-packages@claude-scientific-skills)

auto-animate

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skills-collection-manager

Comprehensive toolkit for managing large Claude Code skill collections including bulk downloading from GitHub, organizing into categories, detecting and removing duplicates, consolidating skills, and maintaining clean skill repositories with 100+ skills.

cloudflare-durable-objects

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cloudflare-full-stack-scaffold

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sequential-thinking

Systematic step-by-step reasoning with revision and branching. Use for complex problems, multi-stage analysis, design planning, problem decomposition, or encountering unclear scope, alternative approaches needed, revision requirements.

skill-harvester

Meta-skill for extracting and creating reusable Claude Code skills from past work sessions. Analyzes git history, code patterns, workflows, and documentation to identify harvestable skills, then generates comprehensive skill definitions with best practices, examples, and structured templates.

cloudflare-r2

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session-timeout-handler

Build timeout-resistant Claude Code workflows with chunking strategies, checkpoint patterns, progress tracking, and resume mechanisms to handle 2-minute tool timeouts and ensure reliable completion of long-running operations.

cloudflare-turnstile

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session-launcher

Restores full context when user says "hi-ai" or starts a new conversation. Searches project files, loads memory indexes, reads session state, and creates visual dashboard showing current project, recent decisions, active blockers, and quick actions. Use when user says "hi-ai", "continue", "restore context", or starts a fresh conversation.

condition-based-waiting

Use when tests have race conditions, timing dependencies, or inconsistent pass/fail behavior - replaces arbitrary timeouts with condition polling to wait for actual state changes, eliminating flaky tests from timing guesses

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.

cloudflare-hyperdrive

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cloudflare-worker-base

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browser-app-creator

Creates complete single-file HTML/CSS/JS web apps with localStorage persistence, ADHD-optimized UI (60px+ buttons), dark mode, and offline functionality. Use when user says "create app", "build tool", "make dashboard", or requests any browser-based interface.

cloudflare-d1

Cloudflare D1 SQLite database with Workers, Drizzle ORM, migrations

cloudflare-vectorize

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hono-routing

Build type-safe APIs with Hono for Cloudflare Workers, Deno, Bun, Node.js. Routing, middleware, validation (Zod/Valibot), RPC, streaming (SSE), WebSocket, security (CSRF, secureHeaders). Use when: building Hono APIs, streaming SSE, WebSocket, validation, RPC. Troubleshoot: validation hooks, RPC types, middleware chains, JWT verify algorithm required (v4.11.4+), body consumed errors.

testing-builder

Automatically generates comprehensive test suites (unit, integration, E2E) based on code and past testing patterns. Use when user says "write tests", "test this", "add coverage", or after fixing bugs to create regression tests. Eliminates testing friction for ADHD users.

context-manager

Manages permanent memory storage for decisions, blockers, context, preferences, and procedures. Use when user says "remember", "save this decision", "what did we decide", "recall", "search memories", "any blockers", or when making important architectural decisions. Provides SDAM compensation through external memory.

cloudflare-queues

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cloudflare-kv

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scientific-writing

Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.

infrastructure-skill-builder

Transform infrastructure documentation, runbooks, and operational knowledge into reusable Claude Code skills. Convert Proxmox configs, Docker setups, Kubernetes deployments, and cloud infrastructure patterns into structured, actionable skills.

tanstack-query

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cloudflare-images

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json-config-helper

Validate, format, and work with JSON configuration files

react-hook-form-zod

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biomni

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

csv-data-summarizer

Analyzes CSV files, generates summary stats, and plots quick visualizations using Python and pandas.

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.

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.

sveltia-cms

Sveltia CMS Git-backed content management (Decap/Netlify CMS successor). 5x smaller bundle (300 KB), GraphQL performance, solves 260+ issues. Use for static sites (Hugo, Jekyll, 11ty, Gatsby, Astro, Next.js), blogs, docs, i18n, or encountering OAuth errors, TOML/YAML issues, CORS problems, content listing errors.

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.

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.

using-git-worktrees

Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory selection and safety verification

zinc-database

Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.

frontend-dev-guidelines

Opinionated frontend development standards for modern React + TypeScript applications. Covers Suspense-first data fetching, lazy loading, feature-based architecture, MUI v7 styling, TanStack Router, performance optimization, and strict TypeScript practices.

vercel-kv

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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.

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.

scanpy

Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.

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.

code-review

Review code changes against pplx-sdk architecture conventions, type safety, error handling, and testing standards.

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.

multi-ai consultant

Consult external AIs (Gemini 2.5 Pro, OpenAI Codex, Claude) for second opinions. Use for debugging failures, architectural decisions, security validation, or need fresh perspective with synthesis.

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.

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.

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.

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.

wordpress-plugin-core

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d3-viz

Creating interactive data visualisations using d3.js. This skill should be used when creating custom charts, graphs, network diagrams, geographic visualisations, or any complex SVG-based data visualisation that requires fine-grained control over visual elements, transitions, or interactions. Use this for bespoke visualisations beyond standard charting libraries, whether in React, Vue, Svelte, vanilla JavaScript, or any other environment.

content-collections

Production-tested setup for Content Collections - a TypeScript-first build tool that transforms local content files (Markdown/MDX) into type-safe data collections with automatic validation. Use when: building blogs, documentation sites, or content-heavy applications with Vite + React, setting up MDX content with React components, implementing type-safe content schemas with Zod, migrating from Contentlayer, or encountering TypeScript import errors with content collections. Covers: Vite plugin setup, tsconfig path aliases, collection schemas with Zod validation, MDX compilation with compileMDX, transform functions for computed properties, rehype/remark plugins, React component integration with MDXContent, Cloudflare Workers deployment, and production build optimization. Keywords: content-collections, @content-collections/core, @content-collections/vite, @content-collections/mdx, MDX, markdown, Zod schema validation, type-safe content, frontmatter, compileMDX, defineCollection, defineConfig, Vite plugin, tsconfig paths, .content-collections/generated, MDXContent component, rehype plugins, remark plugins, content schema, document transform, allPosts import, static site generation, blog setup, documentation, Cloudflare Workers static assets, content validation errors, module not found content-collections, path alias not working, MDX type errors, transform function async, collection not updating

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.

tinacms

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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.

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.

fastmcp

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molfeat

Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

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.

typescript-mcp

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pubchem-database

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

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).

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.

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

playwright browser automation

Complete browser automation with Playwright. Auto-detects dev servers, writes clean test scripts to /tmp. Test pages, fill forms, take screenshots, check responsive design, validate UX, test login flows, check links, automate any browser task. Use when user wants to test websites, automate browser interactions, validate web functionality, or perform any browser-based testing.

gget

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

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. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.

skill-creator

Creates new Claude Code skills following repository conventions with proper structure, frontmatter, workflows, code examples, and reference files. Use when users request "create a skill", "new skill", "generate skill", or "add skill to collection".

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.

using-superpowers

Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions. Part of SuperNavigator App Layer.

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.

fluxwing component expander

Add interaction states like hover, focus, disabled, active, error to existing uxscii components. Use when working with .uxm files, when user wants to expand, enhance, or add states to .uxm components.

fluxwing component creator

Create uxscii components with ASCII art and structured metadata when user wants to create, build, or design UI components. Use when working with .uxm files, when user mentions .uxm components, or when creating buttons, inputs, cards, forms, modals, or navigation.

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.

pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

medchem

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

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.

cloudflare-workflows

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github-project-automation

This skill provides comprehensive automation for GitHub repository setup and configuration. It should be used when creating new projects, setting up CI/CD pipelines, configuring issue templates, enabling security scanning, or migrating existing projects to GitHub automation. The skill prevents 18 documented errors in GitHub Actions YAML syntax, workflow configuration, issue template structure, Dependabot setup, and CodeQL security scanning. It includes 12 production-tested workflow templates, 4 issue templates, security configurations, and automation scripts for rapid project setup. Use when: setting up GitHub Actions CI/CD, creating issue/PR templates, enabling Dependabot, configuring CodeQL scanning, automating GitHub repository setup, fixing YAML syntax errors, integrating security scanning, deploying to Cloudflare Workers via GitHub Actions, or implementing multi-framework testing matrices. Keywords: github actions, github workflow, ci/cd, issue templates, pull request templates, dependabot, codeql, security scanning, yaml syntax, github automation, repository setup, workflow templates, github actions matrix, secrets management, branch protection, codeowners, github projects, continuous integration, continuous deployment, workflow syntax error, action version pinning, runner version, github context, yaml indentation error

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.

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.

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

docs-seeker

Searching internet for technical documentation using llms.txt standard, GitHub repositories via Repomix, and parallel exploration. Use when user needs: (1) Latest documentation for libraries/frameworks, (2) Documentation in llms.txt format, (3) GitHub repository analysis, (4) Documentation without direct llms.txt support, (5) Multiple documentation sources in parallel

claude-api

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paper-2-web

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

scientific-visualization

Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.

ai-sdk-core

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browser daemon

Persistent browser automation via Playwright daemon. Keep a browser window open and send it commands (navigate, execute JS, inspect console). Perfect for interactive debugging, development, and testing web applications. Use when you need to interact with a browser repeatedly without opening/closing it.

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.

uniprot-database

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.

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.

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.

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.

test-driven-development

Use when implementing any feature or bugfix, before writing implementation code

uspto-database

Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.

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.

google-gemini-embeddings

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biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

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.

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.

dask

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

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.

statsmodels

Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.

codex

Use when the user asks to run Codex CLI (codex exec, codex resume) or references OpenAI Codex for code analysis, refactoring, or automated editing. Uses GPT-5.2 by default for state-of-the-art software engineering.

literature-review

Assistance with writing literature reviews by searching for academic sources via Semantic Scholar, OpenAlex, Crossref and PubMed APIs. Use when the user needs to find papers on a topic, get details for specific DOIs, or draft sections of a literature review with proper citations.

cloudflare-browser-rendering

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backend-dev-guidelines

Comprehensive backend development guide for Langfuse's Next.js 14/tRPC/Express/TypeScript monorepo. Use when creating tRPC routers, public API endpoints, BullMQ queue processors, services, or working with tRPC procedures, Next.js API routes, Prisma database access, ClickHouse analytics queries, Redis queues, OpenTelemetry instrumentation, Zod v4 validation, env.mjs configuration, tenant isolation patterns, or async patterns. Covers layered architecture (tRPC procedures → services, queue processors → services), dual database system (PostgreSQL + ClickHouse), projectId filtering for multi-tenant isolation, traceException error handling, observability patterns, and testing strategies (Jest for web, vitest for worker).

tooluniverse

Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

fluxwing screen scaffolder

Build complete UI screens by composing multiple uxscii components. Use when working with .uxm files, when user wants to create, scaffold, or build .uxm screens like login, dashboard, profile, settings, or checkout pages.

testing-skills-with-subagents

Use when creating or editing skills, before deployment, to verify they work under pressure and resist rationalization - applies RED-GREEN-REFACTOR cycle to process documentation by running baseline without skill, writing to address failures, iterating to close loopholes

tdd-reference

pict-test-designer

Design comprehensive test cases using PICT (Pairwise Independent Combinatorial Testing) for any piece of requirements or code. Analyzes inputs, generates PICT models with parameters, values, and constraints for valid scenarios using pairwise testing. Outputs the PICT model, markdown table of test cases, and expected results.

writing-plans

Use when you have a spec or requirements for a multi-step task, before touching code

databases

Work with MongoDB (document database, BSON documents, aggregation pipelines, Atlas cloud) and PostgreSQL (relational database, SQL queries, psql CLI, pgAdmin). Use when designing database schemas, writing queries and aggregations, optimizing indexes for performance, performing database migrations, configuring replication and sharding, implementing backup and restore strategies, managing database users and permissions, analyzing query performance, or administering production databases.

rdkit

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

labarchive-integration

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

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.

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.

hypogenic

Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

repomix

Package entire code repositories into single AI-friendly files using Repomix. Capabilities include pack codebases with customizable include/exclude patterns, generate multiple output formats (XML, Markdown, plain text), preserve file structure and context, optimize for AI consumption with token counting, filter by file types and directories, add custom headers and summaries. Use when packaging codebases for AI analysis, creating repository snapshots for LLM context, analyzing third-party libraries, preparing for security audits, generating documentation context, or evaluating unfamiliar codebases.

alphafold-database

Access AlphaFold 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.

openai-api

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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.

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.

subagent-driven-development

Use when executing implementation plans with independent tasks in the current session

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.

umap-learn

UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

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.

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.

defense-in-depth

Apply layered security architecture. Use when designing security controls, hardening systems, or reviewing security posture. Covers multiple security layers.

fluxwing component viewer

View detailed information about a specific uxscii component including metadata, states, props, and ASCII preview. Use when working with .uxm files, when user wants to see, view, inspect, or get details about a .uxm component.

pathml

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.

verification-before-completion

Run verification commands and confirm output before claiming success. Use when about to claim work is complete, fixed, or passing, before committing or creating PRs.

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.

ai-multimodal

Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.

web-frameworks

Build modern full-stack web applications with Next.js (App Router, Server Components, RSC, PPR, SSR, SSG, ISR), Turborepo (monorepo management, task pipelines, remote caching, parallel execution), and RemixIcon (3100+ SVG icons in outlined/filled styles). Use when creating React applications, implementing server-side rendering, setting up monorepos with multiple packages, optimizing build performance and caching strategies, adding icon libraries, managing shared dependencies, or working with TypeScript full-stack projects.

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.

testing-anti-patterns

Use when writing or changing tests, adding mocks, or tempted to add test-only methods to production code - prevents testing mock behavior, production pollution with test-only methods, and mocking without understanding dependencies

pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

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.

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.

shopify

Enables Claude to manage Shopify store operations, products, and orders

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.

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.

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.

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.

openai-responses

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openai-agents

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anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

ai-sdk-ui

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template-skill

Replace with description of the skill and when Claude should use it.

fluxwing screenshot importer

Import UI screenshots and generate uxscii components automatically using vision analysis. Use when user wants to import, convert, or generate .uxm components from screenshots or images.

pymoo

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

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.

clerk-auth

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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.

seaborn

Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.

latchbio-integration

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

media-processing

Process multimedia files with FFmpeg (video/audio encoding, conversion, streaming, filtering, hardware acceleration), ImageMagick (image manipulation, format conversion, batch processing, effects, composition), and RMBG (AI-powered background removal). Use when converting media formats, encoding videos with specific codecs (H.264, H.265, VP9), resizing/cropping images, removing backgrounds from images, extracting audio from video, applying filters and effects, optimizing file sizes, creating streaming manifests (HLS/DASH), generating thumbnails, batch processing images, creating composite images, or implementing media processing pipelines. Supports 100+ formats, hardware acceleration (NVENC, QSV), and complex filtergraphs.

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.

reportlab

PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.

google-gemini-api

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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.

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.

string-database

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.

deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

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.

youtube-downloader

Download YouTube videos with customizable quality and format options. Use this skill when the user asks to download, save, or grab YouTube videos. Supports various quality settings (best, 1080p, 720p, 480p, 360p), multiple formats (mp4, webm, mkv), and audio-only downloads as MP3.

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.

route-tester

Test authenticated routes in the your project using cookie-based authentication. Use this skill when testing API endpoints, validating route functionality, or debugging authentication issues. Includes patterns for using test-auth-route.js and mock authentication.

root-cause-tracing

Systematically trace bugs backward through call stack to find original trigger. Use when errors occur deep in execution and you need to trace back to find the original trigger.

neon-vercel-postgres

Neon + Vercel serverless Postgres for edge and serverless environments. Use for Cloudflare Workers, Vercel Edge, Next.js apps with HTTP/WebSocket connections, database branching (git-like), Drizzle/Prisma ORM integration, migrations, PITR backups, or encountering connection pool exhausted errors, TCP connection issues, SSL config problems.

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.

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.

finishing-a-development-branch

Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured options for merge, PR, or cleanup

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.

torch-geometric

Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

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.

pymc-bayesian-modeling

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

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.

error-tracking

Implement error tracking with Sentry for automatic exception monitoring, release tracking, and performance issues. Use when setting up error monitoring, tracking bugs in production, or analyzing application stability.

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.

better-auth

Implement authentication and authorization with Better Auth - a framework-agnostic TypeScript authentication framework. Features include email/password authentication with verification, OAuth providers (Google, GitHub, Discord, etc.), two-factor authentication (TOTP, SMS), passkeys/WebAuthn support, session management, role-based access control (RBAC), rate limiting, and database adapters. Use when adding authentication to applications, implementing OAuth flows, setting up 2FA/MFA, managing user sessions, configuring authorization rules, or building secure authentication systems for web applications.

elevenlabs-agents

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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.

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.

cloudflare-mcp-server

Build MCP (Model Context Protocol) servers on Cloudflare Workers with tools, resources, and prompts.

vercel-blob

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executing-plans

Use when you have a written implementation plan to execute in a separate session with review checkpoints

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.

sharing-skills

Use when you've developed a broadly useful skill and want to contribute it upstream via pull request - guides process of branching, committing, pushing, and creating PR to contribute skills back to upstream repository

fluxwing library browser

Browse and view all available uxscii components including bundled templates, user components, and screens. Use when working with .uxm files, when user wants to see, list, browse, or search .uxm components or screens.

openai-assistants

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matplotlib

Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

api-integration-builder

Create new API service integrations for Leavn - REST clients, CloudKit, Bible APIs with proper error handling and caching

open-source-contributions

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mcp-builder

Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).