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.
npx skills add majiayu000/claude-skill-registry --skill 29-regulatory-community-chia-pet --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Protein-Mediated Regulatory Community Analysis from ChIA-PET ## 1. Overview Main steps include: - Refer to the **Inputs & Outputs** section to check available inputs and design the output structure. - Standardize the information contained in the BED format peak file. - Build a chromatin interaction network where: - nodes = protein binding sites (peaks) - edges = protein-mediated loops. - Detect regulatory communities (3D modules) using graph clustering. - Prioritize hub anchors using network centrality. - Visualize the largest regulatory communities. Tools called in this skill: - `mcp__igraph-tools__build_chromatin_network` - `mcp__igraph-tools__analyze_chromatin_network` - `mcp__igraph-tools__plot_chromatin_communities` --- ## 2. When to use this skill Use this skill when you have ChIA-PET data in BEDPE and BED format and you want to: - Reveal **regulatory communities** (3D modules) formed by: - promoters - enhancers - other regulatory elements - Identify **hub anchors** (peaks involved in many interactions) for a particular protein. - Study **protein-mediated rewiring** of chromatin structure between conditions by comparing networks. - Generate interpretable **network visualiza
- 1. Overview
- 2. When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision tree
- Step 1: Standardize the information contained in the BED format peak file
- Step 2: Build the Chromatin Interaction Network
- Step 2: Detect Communities and Compute Network Centrality
- Step 3 — Visualize Top Regulatory Communities
ChIA_PET_community/ communities/ plots/ temp/
What does the regulatory-community-analysis-ChIA-PET skill do?
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 29-regulatory-community-chia-pet --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.