This repository contains scripts for performing the following analyses, organized into the corresponding subfolders:
CHART — Scripts from FASTQ quality control to CHART peak calling and differential analysis.
Compartment analysis — Scripts using dcHiC to identify differential compartments and subcompartments.
CTCF Cut&Run analysis — Scripts from FASTQ quality control to CTCF peak calling and differential analysis.
Loop analysis — Scripts from FASTQ quality control through Mustache loop calling and differential analysis.
RNA-seq — Scripts from STAR alignment to differential gene expression analysis.
TAD analysis — Scripts to calculate insulation scores, identify differential domains, and classify domain subtypes.