├── Analysis ├── Fig3_Inter_chromosomal_interaction.ipynb ├── Fig4_Genome_contact_distance.ipynb ├── Fig4_Span_Compartments.ipynb ├── Fig4_Span_TADs.ipynb ├── Fig4_calculate_enrichment_score_of_specific_kmer.ipynb ├── Fig4s_Span_loops_distribution.ipynb ├── Fig5_GM12878_doublebell_TAD.ipynb ├── Fig5_subTAD_fanc_plot.ipynb ├── Fig6_GM12878_example_TAD.ipynb ├── Fig6_b_globin_in_K562.ipynb ├── Fig6_b_globin_locus_in_GM12878.ipynb ├── Fig7_loop_anchor_methylation_corr.ipynb ├── README.md └── pickle_summary.py ├── Generate_Pairwise_contact_juicematrix.py ├── LICENSE ├── README.md └── Scripts ├── Alignment.sh ├── Fragment_Annotation.sh ├── Fragment_Annotation_linux.sh ├── Generate_Pairwise_contact_juicematrix.py ├── Read_Fragment_Annotation.py ├── Read_Fragment_Annotation_for_Dnase.py ├── minimap2_subreads_remapping.sh └── multichrom_check.sh /Analysis/Fig3_Inter_chromosomal_interaction.ipynb: -------------------------------------------------------------------------------- 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