hic-loop-calling
CommunityDetect Hi-C chromatin loops from mcool data.
AuthorBIsnake2001
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Chromatin loop detection from Hi-C data is complex and multi-step, requiring input validation, coordinate harmonization, data extraction, and loop identification. This skill automates a reproducible workflow to detect loops from Hi-C data stored in .mcool/.cool/.hic formats, delivering loop calls and preparation views for visualization.
Core Features & Use Cases
- End-to-end loop calling workflow starting from processed Hi-C inputs.
- Harmonizes chromosome names to the "chr" convention and generates chromosome-arm views for downstream analyses.
- Extracts contact matrices at a user-selected resolution and outputs BEDPE loop calls alongside supporting view files.
- Use case: starting from a .mcool file, call loops at 5 kb resolution and produce ${sample}_loop_calling/loops/${sample}_loops_5000.bedpe plus temporary view files for IGV.
Quick Start
Provide sample name, genome assembly, and Hi-C data path (.mcool/.cool/.hic) to run the loop-calling workflow and generate outputs.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: hic-loop-calling Download link: https://github.com/BIsnake2001/ChromSkills/archive/main.zip#hic-loop-calling Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 223,000+ vetted skills library on demand.