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hic-matrix-qc

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Hi-C matrix QC across replicates and resolution.

Data & Analytics#replicate#matrix#qc#hic#cooltools#cooler#genome
AuthorBIsnake2001
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This QC skill assesses Hi-C data quality by computing coverage, cis/trans ratios, and distance-dependent contact decay (P(s)) for .cool, .mcool, or .hic inputs, enabling reliable downstream analyses.

Core Features & Use Cases

  • Compute per-bin coverage and cis/trans ratios at a user-specified resolution.
  • Generate P(s) curves and decay plots to evaluate contact frequency as a function of genomic distance.
  • Compare replicates via correlation metrics to identify inconsistencies and assess experimental reproducibility.
  • Output a structured QC directory with logs, metrics, and plots suitable for reporting.

Quick Start

Run hic-matrix-qc on your Hi-C files to generate QC metrics and plots for your chosen resolution.

Dependency Matrix

Required Modules

None required

Components

Standard package

đź’» 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-matrix-qc
Download link: https://github.com/BIsnake2001/ChromSkills/archive/main.zip#hic-matrix-qc

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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