Compartment shift Analysis

Overview

This skill performs A/B compartment shift analysis using PC1 eigenvector values extracted from Hi-C data, following the HOMER framework. It supports two conditions, each with two or more replicates, and uses the PC1 values (E1 column) from user-provided TSV files.

Major steps include:

• Refer to Inputs & Outputs to verify necessary files.
• Always prompt user for genome assembly used. Never decide by yourself.
• 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.

When to use this skill