fix-review
Verify fix commits address security findings without introducing new bugs or regressions. Analyzes diffs for anti-patterns like removed validation, weakened access control, reduced error handling, reordered external calls, and changed integer operations. Generates structured FIX_REVIEW_REPORT with finding status tracking.
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.
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.
flutter-expert
Flutter and Dart expert including widgets, state management, and platform integration
form-and-actions-in-sveltekit
Describes Form and Actions implementations.
form-validation-with-zod
Enforces the use of Zod for form validation throughout the project.
forum-monitor
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framework-context
Load and synthesize framework architecture context for reflection and planning tasks.
frontend-expert
Frontend development expert including UI/UX patterns, responsive design, and accessibility
function-length-and-responsibility
This rule enforces the single responsibility principle, ensuring functions are short and focused.
gamedev-expert
Game development expert including DragonRuby, Unity, and game mechanics
gap-detection
Detect missing docs, undocumented files, project health issues, and coverage gaps on session start or on-demand. Scans for README gaps, TODO/FIXME counts, and test coverage holes.
gcloud-cli
Google Cloud CLI operations and resource management
gemini-cli-security
AI-powered code vulnerability analysis and dependency scanning using Gemini CLI security extension patterns. Detects hardcoded secrets, injection attacks, weak cryptography, authentication flaws, and LLM prompt injection. Also scans dependencies against the OSV.dev vulnerability database.
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.
generate-image
Generate or edit images using AI models (FLUX, Gemini). 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.
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.
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.
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.
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.
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.
git-expert
Advanced Git operations wrapper. Optimizes token usage by guiding complex git workflows into efficient CLI commands.
github-mcp
GitHub API operations - repositories, issues, pull requests, actions, code security, discussions, gists, and more. Use for GitHub-related tasks like managing PRs, issues, searching code, and monitoring workflows.
github-ops
Workflow for repository reconnaissance and operations using GitHub CLI (gh). Optimizes token usage by using structured API queries instead of blind file fetching.
gitops-workflow
Implement GitOps workflows with ArgoCD and Flux for automated, declarative Kubernetes deployments with continuous reconciliation. Use when implementing GitOps practices, automating Kubernetes deployments, or setting up declarative infrastructure management.
goal-backward-verification
Verify that task outputs actually achieve stated goals through 4 progressive levels of verification
go-expert
Go programming expert including APIs, gRPC, concurrency, and best practices
google-workspace
Google Workspace integration skill for Gmail, Calendar, Drive, Docs, and Sheets via Python client libraries and MCP servers
graphql-expert
GraphQL expert including schema design, Apollo Client/Server, and caching
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.
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.
heartbeat
Start and manage the full heartbeat ecosystem for agent-studio. Registers all 7 heartbeat loops plus auto-reschedule task via CronCreate to keep the agent ecosystem healthy, indexed, informed, and connected.
helm-chart-scaffolding
Design, organize, and manage Helm charts for templating and packaging Kubernetes applications with reusable configurations. Use when creating Helm charts, packaging Kubernetes applications, or implementing templated deployments.
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.
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.
hook-creator
Creates and registers hooks for the Claude Code framework. Handles pre/post tool execution, validation, memory, and session hooks. Use when new validation, safety, or automation hooks are needed.
html-tailwind-css-and-javascript-expert-rule
Sets the AI to act as an expert in HTML, Tailwind CSS, and vanilla JavaScript, focusing on clarity and readability for all HTML, JS, and CSS files.
htmx-expert
HTMX expert including hypermedia patterns, Django/Flask integration
huggingface
Hugging Face Hub operations, model inference, dataset management, PEFT/LoRA fine-tuning, and Spaces deployment via MCP tools and Python APIs
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.
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.
imagen-generation
Google Imagen image generation via Vertex AI — text-to-image, image editing, inpainting, and upscaling using ImageGenerationModel
implementation-readiness
Gate for HIGH/EPIC tasks that validates plan completeness and architecture compliance before implementation begins
incident-runbook-templates
Create structured incident response runbooks with step-by-step procedures, escalation paths, and recovery actions. Use when building runbooks, responding to incidents, or establishing incident response procedures.
init
Auto-evolution skill to initialize a new repository with AGENTS.md localized context.
insecure-defaults
Detect hardcoded credentials, default passwords, fail-open configurations, insecure default settings, and other security misconfigurations that ship as default behavior in applications.
insight-extraction
Extract actionable insights from completed coding sessions. Use when a session completes to capture learnings for future sessions.
instinct-learning
Records atomic learned behaviors with confidence scores. Project-scoped instincts are isolated per project and auto-promote to global scope at confidence threshold 0.8. Stores instincts in .claude/context/memory/instincts.jsonl
interactive-requirements-gathering
Structured interactive questionnaire framework for gathering requirements from users. Uses A/B/C/D/E multiple choice patterns with additive vs exclusive question classification.
ios-expert
iOS development expert including SwiftUI, UIKit, and Apple frameworks
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