UMR-LMR-PMD-detection
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. The pipeline provides high-resolution enhancer-like LMRs, promoter-associated UMRs, and large-scale PMDs characteristic of reprogramming, aging, or cancer methylomes, enabling integration with chromatin accessibility, TF binding, and genome architecture analyses.
correlation-methylation-epiFeatures
This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.
notion-meeting-intelligence
Prepares meeting materials by gathering context from Notion, enriching with Claude research, and creating both an internal pre-read and external agenda saved to Notion. Helps you arrive prepared with comprehensive background and structured meeting docs.
atac-footprinting
This skill performs transcription factor (TF) footprint analysis using TOBIAS on ATAC-seq data. It corrects Tn5 sequence bias, quantifies TF occupancy at motif sites, generates footprint scores, and optionally compares differential TF binding across conditions.
regulatory-community-analysis-ChIA-PET
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) from ChIA-PET experiment and you want to identify the protein-mediated regulatory community according to the BED and BEDPE file from ChIA-PET.
obsidian-markdown
Create and edit Obsidian Flavored Markdown with wikilinks, embeds, callouts, properties, and other Obsidian-specific syntax. Use when working with .md files in Obsidian, or when the user mentions wikilinks, callouts, frontmatter, tags, embeds, or Obsidian notes.
2agent
Configures 2-Agent workflow between PM and implementation roles. Use when user mentions 2-Agent setup, PM coordination, Cursor setup, or 2-agent operations. Do NOT load for: solo operation, workflow execution, or handoff processing.
competitive-ads-extractor
Extracts and analyzes competitors' ads from ad libraries (Facebook, LinkedIn, etc.) to understand what messaging, problems, and creative approaches are working. Helps inspire and improve your own ad campaigns.
2d-bin-packing
When the user wants to pack 2D rectangular items into bins, optimize 2D cutting patterns, or minimize material waste in 2D packing. Also use when the user mentions "2D packing," "rectangular packing," "sheet packing," "2D bin packing problem," "guillotine cutting," "two-dimensional packing," or "rectangle packing optimization." For 1D problems, see 1d-cutting-stock. For 3D problems, see 3d-bin-packing.
2d-cutting-stock
When the user wants to cut 2D sheets optimally, minimize waste in rectangular sheet cutting, or solve two-dimensional cutting stock problems. Also use when the user mentions "2D cutting," "sheet cutting optimization," "panel cutting," "glass cutting," "steel plate cutting," "guillotine cutting patterns," "two-stage cutting," or "2D trim loss." For 1D problems, see 1d-cutting-stock. For bin packing, see 2d-bin-packing. For irregular shapes, see nesting-optimization.
2d-games
2D game development principles. Sprites, tilemaps, physics, camera.
slack-gif-creator
Toolkit for creating animated GIFs optimized for Slack, with validators for size constraints and composable animation primitives. This skill applies when users request animated GIFs or emoji animations for Slack from descriptions like "make me a GIF for Slack of X doing Y".
raffle-winner-picker
Picks random winners from lists, spreadsheets, or Google Sheets for giveaways, raffles, and contests. Ensures fair, unbiased selection with transparency.
build
Build features with AI coding tools (Claude Code, Lovable, Replit, Cursor). Use when implementing specs, iterating on AI code, or choosing tools. Focuses on tool selection, effective prompting, and iteration workflows for non-technical founders.
3-identifying-architecture
Third step in building instruction context for codebase
peak-calling
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
prioritize
Prioritize tasks and issues to determine what to work on and in what order. Use after identification, when planning work, or when unsure what to do next. This is the third system in the 5-system framework.
30-analyze-impact-150
[30] ANALYZE. Understand how changes impact the system — what's the core, what's affected, what depends on what. Use when planning changes, analyzing systems, debugging issues, or anytime you need to see the full picture of cause and effect. Triggers on \"what's affected\", \"impact analysis\", \"dependencies\", \"scope mapping\", or when you need to understand ripple effects.
40-plan-action-150
[40] PLAN. Create clear action plans with steps, success criteria, and risk awareness. Use before implementing features, making changes, starting projects, or anytime you need a roadmap to success. Triggers on \"plan this\", \"how should we approach\", \"what's the strategy\", \"steps to complete\", or when facing complex multi-step work.
hic-matrix-qc
This skill performs standardized quality control (QC) on Hi-C contact matrices stored in .mcool or .cool format. It computes coverage and cis/trans ratios, distance-dependent contact decay (P(s) curves), coverage uniformity, and replicate correlation at a chosen resolution using cooler and cooltools. Use it to assess whether Hi-C data are of sufficient quality for downstream analyses such as TAD calling, loop detection, and compartment analysis.
302ai-api-integration
ALWAYS use this skill when user needs ANY API functionality (AI models, image generation, video, audio, text processing, etc.). Automatically search 302.AI's 1400+ APIs and generate integration code. Use proactively whenever APIs or AI capabilities are mentioned.
31-analyze-think-150
[31] ANALYZE. Universal deep thinking methodology for any situation requiring quality reasoning. Use when solving problems, debugging, making decisions, analyzing code, planning, reviewing, or anytime you need thorough thinking instead of surface-level responses. Triggers on \"think deeply\", \"analyze thoroughly\", \"reason carefully\", \"deep thinking\", \"understand completely\", or any task requiring careful thought.
nested-TAD-detection
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and resolution, converts the data to a dense matrix, runs OnTAD, and organizes TAD calls and logs for downstream 3D genome analysis.
32-analyze-verify-150
[32] ANALYZE. Ensure every critical claim has verifiable evidence with confidence levels. Each fact must have source + confidence percentage. If confidence <85%, enter Loop150 to find more sources. Use for critical decisions, factual claims, legal/compliance work, or any situation where unverified claims are dangerous.
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
loop-annotation
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
33GOD System Expert
Deep knowledge expert for the 33GOD agentic pipeline system, understands component relationships and suggests feature implementations based on actual codebase state
webapp-testing
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
37signals-rails-style
Apply 37signals/DHH Rails conventions when writing Ruby on Rails code. Use when building Rails applications, reviewing Rails code, or making architectural decisions. Covers various aspects of Rails application architecture, design and dependencies.
skill-share
A skill that creates new Claude skills and automatically shares them on Slack using Rube for seamless team collaboration and skill discovery.
3d-bin-packing
When the user wants to pack 3D boxes into containers, optimize 3D space utilization, or solve container loading problems. Also use when the user mentions "3D packing," "container packing," "box packing," "3D bin packing problem," "cube packing," "three-dimensional packing," "cargo loading," or "space optimization." For pallet-specific loading, see pallet-loading. For container logistics, see container-loading-optimization.
building-mechanics
Three.js 3D building system with spatial indexing, structural physics, and multiplayer networking. Use when creating survival games, sandbox builders, or any game with player-constructed structures. Covers performance optimization (spatial hash grids, octrees, chunk loading), structural validation (arcade/heuristic/realistic physics modes), and multiplayer sync (delta compression, client prediction, conflict resolution).
3d-building-mechanics
Complete Three.js building system with spatial indexing, structural physics, and multiplayer networking. Use for survival/crafting games, sandbox games, multiplayer construction, or any 3D building mechanics.
3d-cv-labeling-2026
Expert in 3D computer vision labeling tools, workflows, and AI-assisted annotation for LiDAR, point clouds, and sensor fusion. Covers SAM4D/Point-SAM, human-in-the-loop architectures, and vertical-specific training strategies. Activate on '3D labeling', 'point cloud annotation', 'LiDAR labeling', 'SAM 3D', 'SAM4D', 'sensor fusion annotation', '3D bounding box', 'semantic segmentation point cloud'. NOT for 2D image labeling (use clip-aware-embeddings), general ML training (use ml-engineer), video annotation without 3D (use computer-vision-pipeline), or VLM prompt engineering (use prompt-engineer).
3d-games
3D game development principles. Rendering, shaders, physics, cameras.
3d-graphics
3D web graphics with Three.js (WebGL/WebGPU). Capabilities: scenes, cameras, geometries, materials, lights, animations, model loading (GLTF/FBX), PBR materials, shadows, post-processing (bloom, SSAO, SSR), custom shaders, instancing, LOD, physics, VR/XR. Actions: create, build, animate, render 3D scenes/models. Keywords: Three.js, WebGL, WebGPU, 3D graphics, scene, camera, geometry, material, light, animation, GLTF, FBX, OrbitControls, PBR, shadow mapping, post-processing, bloom, SSAO, shader, instancing, LOD, WebXR, VR, AR, product configurator, data visualization, architectural walkthrough, interactive 3D, canvas. Use when: creating 3D visualizations, building WebGL/WebGPU apps, loading 3D models, adding animations, implementing VR/XR, creating interactive graphics, building product configurators.
3d-modeling
Expert 3D modeling specialist with deep knowledge of topology, UV mapping, game-ready and film-ready pipelines, DCC tool workflows (Blender, Maya, ZBrush, 3ds Max, Houdini), retopology, LOD systems, and export pipelines. This skill represents years of production experience distilled into actionable guidance. Use when "3d model, 3d modeling, mesh topology, uv unwrap, uv mapping, retopology, retopo, low poly, high poly, subdivision, subdiv, edge flow, edge loops, polygon modeling, box modeling, hard surface, organic modeling, sculpting, zbrush, blender modeling, maya modeling, 3ds max, LOD, level of detail, game ready mesh, film ready, baking normals, high to low, fbx export, gltf export, texel density, 3d, modeling, topology, uv, game-dev, vfx, blender, maya, zbrush, retopology, lod, hard-surface, organic, sculpting" mentioned.
3d-spatial
Use when working in Blender, Unity 3D, Unreal Engine, Cinema 4D, VR/AR applications, or any three-dimensional animation work.
3d-visualizer
Expert in Three.js, 3D graphics, and interactive 3D visualizations
3d-web-experience
Expert in building 3D experiences for the web - Three.js, React Three Fiber, Spline, WebGL, and interactive 3D scenes. Covers product configurators, 3D portfolios, immersive websites, and bringing depth to web experiences. Use when: 3D website, three.js, WebGL, react three fiber, 3D experience.
theme-factory
Toolkit for styling artifacts with a theme. These artifacts can be slides, docs, reportings, HTML landing pages, etc. There are 10 pre-set themes with colors/fonts that you can apply to any artifact that has been creating, or can generate a new theme on-the-fly.
ATACseq-QC
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use this skill when you have filtered BAM file and have called peak for the file. Do NOT use this skill for ChIP-seq data or general alignment statistics.
4-domain-deep-dive
Fourth step in building instruction context for codebase
execute
Execute tasks with velocity and quality. Use when ready to implement after clarity and prioritization are complete. This is the fourth system in the 5-system framework.
security
Protect your SaaS app from common vulnerabilities. Use when building auth, handling user data, or deploying features. Covers authentication, data protection, API security, and OWASP Top 10 for non-technical founders using AI tools.
4-step-program
Coordinator workflow for orchestrating dockeragents through fix-review-iterate-present loop. Use when delegating any task that produces code changes. Ensures agents achieve 10/10 quality before presenting to human.
8bit-docs-patterns
Create documentation with gaming-specific examples, retro styling, and 8-bit terminology. Apply when documenting gaming blocks, RPG components, or retro-styled UI elements.
algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
template-skill
Replace with description of the skill and when Claude should use it.
4claw
4claw — a moderated imageboard for AI agents. Boards, threads, replies, media uploads, bumping (bump=false to not bump), greentext, and automatic capacity purges. Post spicy hot takes (what you're REALLY thinking) — but no illegal content, doxxing, harassment, or minors.
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