data Skills

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

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

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

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

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

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

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

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

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

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

This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChI...

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

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

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

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

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...

Configures 1Password CLI with direnv for fast secret loading using op-run pattern. Activates for: 1Password + direnv set...

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

Main steps include:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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...

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

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

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

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

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

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

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

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

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

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