jupyter-notebook-analysis
Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.
bioinformatics-fundamentals
Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.
claude-collaboration
Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.
claude-skill-management
Expert guide for managing Claude Code global skills and commands. Use when creating new skills, symlinking to projects, updating existing skills, or organizing the centralized skill repository.
data-analysis-patterns
Best practices for data aggregation, recalculation, and category management in scientific analyses. Covers when to recalculate vs reuse aggregated data, handling category changes, and ensuring analytical accuracy.
data-visualization
Best practices for creating clear, accurate scientific visualizations with matplotlib, seaborn, and other Python plotting libraries. Covers common pitfalls, optimization techniques, publication-quality figure generation, and Claude API image size constraints.
documentation-organization
Organize research project documentation - structure working files, prepare sharing packages, maintain clean project layout
scientific-publication
Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.
phylogenetics
Phylogenetic tree analysis, visualization, annotation management, and iTOL troubleshooting
bioinformatics-visualization
Publication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation
command-discipline
Run shell commands bare — no decorative echo headers ("=== X ==="), no echo-then-cmd chains, no trailing "echo done". Use the Bash tool's description field for any narration. Triggers any time you're about to issue a Bash command.
documentation
Best practices for session documentation - incremental summaries, fix reports, and audit trails
systematic-debugging
Structured 4-phase debugging methodology. Use when encountering any bug, test failure, unexpected behavior, or pipeline error — before proposing fixes. Enforces root cause investigation first.
token-efficiency
Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading, command execution, and output handling strategies. Includes model selection guidance (Opus for learning, Sonnet for development/debugging). Prefers bash commands over reading files.
verification-before-completion
Enforces evidence-based completion claims. Use before claiming work is done, tests pass, or bugs are fixed. Requires running verification commands and confirming output before any success claims.
hackmd
HackMD collaborative markdown - slide presentations, embedded SVG diagrams, and real-time editing best practices
project-sharing
Prepare organized packages of project files for sharing at different levels - from summary PDFs to fully reproducible archives. Creates copies with cleaned notebooks, documentation, and appropriate file selection. After creating sharing package, all work continues in the main project directory.
bioservices
Unified Python interface to 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome, PSICQUIC). Best for cross-database analysis, ID mapping, and multi-service workflows. For quick single-database lookups use gget.
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Gene info, BLAST, AlphaFold structures, enrichment analysis, single-cell data, disease associations. Best for interactive exploration and quick lookups. For batch/multi-database Python workflows use bioservices.
gnomad-database
Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance via GraphQL API. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.
galaxy-automation
BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automation project.
galaxy-tool-wrapping
Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools
galaxy-training-material
Expert in Galaxy Training Network (GTN) tutorial development. GTN markdown syntax, special boxes, tool references, snippets, YAML front matter, and best practices for writing and updating training materials in the galaxyproject/training-material repository.
galaxy-workflow-development
Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.
galaxy-workflow-viz
Generate Galaxy-branded workflow visualization SVGs for IWC workflows. Creates static diagrams matching Galaxy's workflow editor style with bezier connections, node cards, and proper terminal positioning. Use when creating visual diagrams for workflows in this repository.
workflow-maintenance-log
Maintain per-workflow developer logs in Obsidian when working on Galaxy workflows. Use whenever creating, version-bumping, fixing, or updating an IWC/Galaxy `.ga` workflow or its `-tests.yml`. Logs detailed changes, test YAML edits, and `planemo` invocation history so the correct planemo command (full `planemo test` vs fast `workflow_test_on_invocation`) is obvious without guessing. Triggers on any session that edits `.ga`, edits `-tests.yml`, runs `planemo test`/`planemo workflow_test_on_invocation`, or prepares an IWC PR.
conda-recipe
Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors
data-backup
Smart automated backup system with skill integration. Detects project type (notebooks, data files, HackMD docs) and applies appropriate cleanup before backup. Rolling daily backups, compressed milestones, and CHANGELOG tracking.
folder-organization
Best practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects
managing-environments
Best practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.
obsidian
Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding notes, creating tasks, and organizing project documentation. Updated with 2025-2026 best practices including MOCs, properties, practical organization patterns, and Obsidian CLI (1.12+).
genomeark-aws
Access and navigate GenomeArk AWS S3 bucket - VGP assemblies, QC data, and species directory structure
vgp-pipeline
VGP assembly pipeline - Galaxy workflow selection, execution patterns, QC checkpoints, and batch orchestration
qa-use
E2E testing and browser automation with qa-use CLI. Use when the user needs to run tests, verify features, automate browser interactions, or debug test failures.
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.
zellij-plugin-dev
Develop Zellij plugins with Rust/WASM, API reference, event system, UI rendering, plugin lifecycle, and real-world examples from diverse open source plugins
web-design-guidelines
Review UI code for Web Interface Guidelines compliance. Use when asked to "review my UI", "check accessibility", "audit design", "review UX", or "check my site against best practices".
unfuck-my-git-state
Diagnose and recover broken Git state and worktree metadata with a staged, low-risk recovery flow. Use when Git reports detached or contradictory HEAD state, phantom worktree locks, orphaned worktree entries, missing refs, 0000000000000000000000000000000000000000 hashes, or branch operations fail with errors like already checked out, unknown revision, not a valid object name, or cannot lock ref.
ui-ux-design
Modern UI/UX design principles, patterns, and best practices for web and mobile applications. Use when building user interfaces, designing layouts, choosing color palettes, implementing responsive design, ensuring accessibility (WCAG), or creating beautiful modern applications. Includes 2026 design trends, Tailwind CSS patterns, Shadcn/ui integration, micro-interactions, and mobile-first responsive design.
temporal-python-testing
Test Temporal workflows with pytest, time-skipping, and mocking strategies. Covers unit testing, integration testing, replay testing, and local development setup. Use when implementing Temporal workflow tests or debugging test failures.
debugging-complex-multi-layer-systems
A reasoning pattern for diagnosing and fixing bugs that span multiple abstraction layers in complex systems.
fal-text-to-image
Generate, remix, and edit images using fal.ai's AI models. Supports text-to-image generation, image-to-image remixing, and targeted inpainting/editing.
agno
Agno AI agent framework. Use for building multi-agent systems, AgentOS runtime, MCP server integration, and agentic AI development.
shadcn-ui
Expert guidance for integrating and building applications with shadcn/ui components, including component discovery, installation, customization, and best practices.
find-skills
Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.
c4-architecture
Generate architecture documentation using C4 model Mermaid diagrams. Use when asked to create architecture diagrams, document system architecture, visualize software structure, create C4 diagrams, or generate context/container/component/deployment diagrams. Triggers include "architecture diagram", "C4 diagram", "system context", "container diagram", "component diagram", "deployment diagram", "document architecture", "visualize architecture".
vercel-react-best-practices
React and Next.js performance optimization guidelines from Vercel Engineering. This skill should be used when writing, reviewing, or refactoring React/Next.js code to ensure optimal performance patterns. Triggers on tasks involving React components, Next.js pages, data fetching, bundle optimization, or performance improvements.
hindsight-memory-governance
DEPRECATED shim. Memory governance is consolidated into the single `hindsight` skill package.
33god-task-triage
Facilitates a single point of ingress for any and all tasks. Used when pulling a new `inbox` task from the 33god plane workspace, or any prompt that explicitly or implicitly describes a non-trivial task. Triggered by `add a feature`, `task.inbox.new` event.
33god
Unified 33GOD master skill and router. Use for any 33GOD request: architecture context, project creation, task execution, coding workflow, service development, workflow generation, and platform-level orchestration. This skill routes to focused references/workflows/scripts for incremental discovery.
Page 1365 of 1630 · 81452 results