data Skills

[02] META. Create new skills when existing ones don't cover the task. Analyze unique requirements, build framework (Frame → Resear...

Personal knowledge base powered by Ensue for capturing and retrieving understanding. Use when user wants to save knowledge, recall...

Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself...

Establish clarity before starting work. Use when beginning any significant task, when input is vague or stream-of-consciousness, o...

Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web...

This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information usin...

Strategic amplification mode that reveals blind spots, untapped opportunities, and hidden leverage points in any business strategy...

Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R...

This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions...

This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak...

This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or A...

This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It pro...

Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existi...

This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools,...

This skill should be used when users need to identify topologically associating domains (TADs) from Hi-C data in .mcools (or .cool...

This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.

Use this skill when working with the 1Password CLI (`op` command) for secrets management, retrieving API keys, injecting secrets i...

Configures 1Password CLI with direnv for fast secret loading using op-run pattern. Activates for: 1Password + direnv setup, slow s...

Secure secret management using 1Password CLI. Detect plaintext secrets in files and codebases, convert environment files to 1Passw...

Main steps include:

Identify friction points, bottlenecks, bugs, and technical debt. Use for audits, debugging sessions, when something feels wrong, o...

Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill)...

This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It c...

[20] UNDERSTAND. Achieve complete clarity on goals, expectations, and success criteria. Use when starting new tasks, when requirem...

This skill performs differential DNA methylation analysis (DMRs and DMCs) between experimental conditions using WGBS methylation t...

[21] UNDERSTAND. Deep research workflow for this project using 150% scope (100% core + 50% boundary), evidence-based reasoning, an...

This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want...

[22] UNDERSTAND. Deep research from all sources — internal (code, git, logs) AND external (web, docs, best practices). Use when ch...

This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with...

[23] UNDERSTAND. Consult external AI models when internal sources are exhausted. Build quality prompts using Prompt150 formula (Co...

This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methyla...

This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analys...

This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylate...

This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K2...

This skill performs transcription factor (TF) footprint analysis using TOBIAS on ATAC-seq data. It corrects Tn5 sequence bias, qua...

This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the co...

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

Creates high-quality content (blog posts, tweets, newsletters, documentation) that matches the user's writing style and voice. Per...

Perform peak calling for ChIP-seq or ATAC-seq data using MACS2, with intelligent parameter detection from user feedback. Use it wh...

Prioritize tasks and issues to determine what to work on and in what order. Use after identification, when planning work, or when...

[30] ANALYZE. Understand how changes impact the system — what's the core, what's affected, what depends on what. Use when planning...

| Server | framework-ts/apps/GameServer/ |

This skill performs standardized quality control (QC) on Hi-C contact matrices stored in .mcool or .cool format. It computes cover...

[31] ANALYZE. Universal deep thinking methodology for any situation requiring quality reasoning. Use when solving problems, debugg...

This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting fr...

[32] ANALYZE. Ensure every critical claim has verifiable evidence with confidence levels. Each fact must have source + confidence...

| Unity project | framework-cs/apps/UnityExample/ |

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