Main steps include:

Second step in building instruction context for codebase

Create and manage project-specific design systems for SaaS applications. Use when starting a new app (CREATE mode), updating an existing design system (MODIFY mode), or building features that need to follow established patterns (WORK WITHIN mode). Outputs to instructions/design-system.md as the single source of truth for all UX/UI decisions.

Identify friction points, bottlenecks, bugs, and technical debt. Use for audits, debugging sessions, when something feels wrong, or before major work to surface hidden issues. This is the second system in the 5-system framework.

Status: ACTIVE

This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.

**Core Principle:** Achieve complete clarity, not just confirm understanding. Know the WHAT, WHY, and HOW of success before acting.

Expert in recreating the legendary 2000s music visualization era - Milkdrop, AVS, Geiss - using modern WebGL and Web Audio APIs.

git remote -v //查看远程状态

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Generated skill from request: pattern emergence detector

Generated skill from request: trinity auto-boot validator

🍆👾 CHAOS SPAWN - Maximum jank energy skill generated from pure chaos

Status: ACTIVE

This skill performs differential DNA methylation analysis (DMRs and DMCs) between experimental conditions using WGBS methylation tracks (BED/BedGraph). It standardizes input files into per-sample four-column Metilene tables, constructs a merged methylation matrix, runs Metilene for DMR detection, filters the results, and generates quick visualizations.

[21] UNDERSTAND. Deep research workflow for this project using 150% scope (100% core + 50% boundary), evidence-based reasoning, and structured investigation notes. Use when the task requires investigation, root-cause analysis, or mapping unknown areas. Always maintain a research log file that captures findings, hypotheses, and next branches; use web.run when external verification is needed.

This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).

**Core Principle:** Research deeply from ALL sources — internal context AND external knowledge. Don't limit yourself to one world.

This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration workflows, using promoter-level methylation–expression relationships.

[23] UNDERSTAND. Consult external AI models when internal sources are exhausted. Build quality prompts using Prompt150 formula (Context + Query + Method + Style). Use when Loop150 exhausts internal sources, need real-world precedents, confidence <75%, or require reasoning from specialized AI models.

name: global-methylation-profile

This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for researchers who want to quantify CpG-level variability across biological samples or conditions, identify highly variable CpGs (HVCs), and explore epigenetic heterogeneity.

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.

씬과 무관하게 Devian BootstrapRoot를 DDOL로 보장한다.

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.

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.

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.

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.

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.

You are an expert in 2D bin packing and rectangular packing optimization. Your goal is to help pack rectangular items into 2D bins or sheets while minimizing waste, number of bins used, or maximizing

You are an expert in two-dimensional cutting stock problems and rectangular sheet optimization. Your goal is to help minimize material waste and costs when cutting large sheets (steel plates, glass pa

2D game development principles. Sprites, tilemaps, physics, camera.

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.

Creates high-quality content (blog posts, tweets, newsletters, documentation) that matches the user's writing style and voice. Performs web research to find citations and supporting evidence. Use when user requests blog posts, marketing content, newsletters, tweets, or any written content that should sound authentic and be well-researched.

Third step in building instruction context for codebase

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 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.

**Core Principle:** Understand the ripple effects. See how changes in one part affect the whole system.

Status: ACTIVE

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.

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.

**Core Principle:** Think deeply, reason thoroughly, understand completely. Quality thinking for any situation.

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. 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.

Status: ACTIVE

This skill performs A/B compartment shift analysis between two Hi-C samples.

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.

Deep knowledge expert for the 33GOD agentic pipeline system, understands component relationships and suggests feature implementations based on actual codebase state

Create your OpenAI Agents SDK skill in one prompt, then learn to improve it throughout the chapter

Status: ACTIVE