Scripts here are for general HiC data analysis, including compartment A/B, domains and loops. Also combine with related ChIP-seq, Factory-RNA-seq and ATAC-seq. Most of the scripts are built on others open source scripts, I just modified a bit and

I used Juicer (https://github.com/aidenlab/juicer) to generate .hic file and convert .hic to .mcool (hic2cool) for higlass (https://github.com/higlass/higlass) to visualize.

Compartment A/B analysis include compartment saddle plot, compartment strength, compartment cloud plot, compartment transition plot, compartment correlation plot and compartment intra-interaction-decay plot.

Loops analysis include detection of loops, anchors analysis(combine with ChIP-seq, GRO-seq and ATAC-seq) and APA plot.

Domians analysis include detection of domains, anchors analysis(combine with ChIP-seq, GRO-seq and ATAC-seq) and insulation score plot.