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hic-compartment-shift

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Detect A/B Hi-C compartment shifts.

Data & Analytics#genomics#hic#homer#differential-analysis#compartment#pc1
AuthorBIsnake2001
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Identify regions where chromatin compartments shift between two conditions by comparing PC1 eigenvectors from Hi-C data.

Core Features & Use Cases

  • Convert TSV (Chrom, start, end, weight, E1) into HOMER-compatible PC1 bedGraph files.
  • Generate a unified genomic bin list for annotatePeaks.
  • Extract PC1 values across all samples.
  • Perform differential PC1 analysis with replicate-aware limma statistics.
  • Produce differential compartment tables and stitched compartment-shift domains.

Quick Start

Provide two condition TSVs with replicates and invoke the analysis to obtain differential PC1 results.

Dependency Matrix

Required Modules

None required

Components

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-compartment-shift
Download link: https://github.com/BIsnake2001/ChromSkills/archive/main.zip#hic-compartment-shift

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