Execute Codex CLI for code analysis, refactoring, and automated code changes. Use when you need to delegate complex code tasks to Codex AI with file references (@syntax) and structured output.

Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields

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

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.

Complete API integration guide for Shopify including GraphQL Admin API, REST Admin API, Storefront API, Ajax API, OAuth authentication, rate limiting, and webhooks. Use when making API calls to Shopify, authenticating apps, fetching product/order/customer data programmatically, implementing cart operations, handling webhooks, or working with API version 2025-10. Requires fetch or axios for JavaScript implementations.

Collection of AWS development skills covering CDK infrastructure as code, cost optimization, and serverless/event-driven architectures with integrated MCP servers.

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.

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

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.

Claude Code plugin enforcing operational guidelines, terse responses, sequential execution, and no destructive operations without confirmation.

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.

Create hierarchical project plans optimized for solo agentic development. Use when planning projects, phases, or tasks that Claude will execute. Produces Claude-executable plans with verification criteria, not enterprise documentation. Handles briefs, roadmaps, phase plans, and context handoffs.

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.

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.

Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).

Keeps IdeaVim documentation in sync with code changes. Use this skill when you need to verify documentation accuracy after code changes, or when checking if documentation (in doc/, README.md, CONTRIBUTING.md) matches the current codebase. The skill can work bidirectionally - from docs to code verification, or from code changes to documentation updates.

Manage Model Context Protocol (MCP) servers - discover, analyze, and execute tools/prompts/resources from configured MCP servers. Use when working with MCP integrations, need to discover available MCP capabilities, filter MCP tools for specific tasks, execute MCP tools programmatically, access MCP prompts/resources, or implement MCP client functionality. Supports intelligent tool selection, multi-server management, and context-efficient capability discovery.

Systematically evaluate code changes for security, correctness, performance, and spec alignment. Use when reviewing PRs, assessing code quality, or verifying implementation against requirements.

This skill should be used when managing the file-based todo tracking system in the todos/ directory. It provides workflows for creating todos, managing status and dependencies, conducting triage, and integrating with slash commands and code review processes.

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.