├── .DS_Store ├── LICENSE ├── README.md ├── data ├── DIPG007_SVs.bed ├── DIPGXIII_SVs.bed ├── GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt ├── GSE63525_K562_Arrowhead_domainlist.txt ├── K562_SVs.bed ├── TADs_chr1 │ ├── GM12878_chr1_50M_domainlist.txt │ ├── chr1_50M_GM12878.h5 │ └── chr1_50M_K562.h5 ├── gold_standard_reorganized_TADs.tsv └── single-TAD │ ├── GM12878_chr1_163500000_165000000_res_10k.txt │ └── K562_chr1_163500000_165000000_res_10k.txt ├── diffdomain-R ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R │ ├── NonZero.R │ ├── comp2domains_by_twtest.R │ ├── comp2domains_by_twtest_parallel.R │ ├── compute_nbins.R │ ├── contact_matrix_from_hic.R │ ├── extractKdiagonalCsrMatrix.R │ ├── makewindow2.R │ ├── normDiffbyMeanSD.R │ ├── sdAdjust.R │ └── twtest_formula.R ├── diffdomain_0.1.0.tar.gz └── man │ ├── NonZero.Rd │ ├── comp2domains_by_twtest.Rd │ ├── comp2domains_by_twtest_parallel.Rd │ ├── compute_nbins.Rd │ ├── contact_matrix_from_hic.Rd │ ├── extractKdiagonalCsrMatrix.Rd │ ├── makewindow2.Rd │ ├── normDiffbyMeanSD.Rd │ ├── sdAdjust.Rd │ └── twtest_formula.Rd ├── diffdomain-py2 ├── diffdomains.py └── domains.py ├── diffdomain-py3 ├── __init__.py ├── classification.py ├── diffdomains.py ├── diffdomains_sv.py ├── subdivide_strength_change.py └── utils.py ├── environment_linux.yml ├── environment_macos.yml ├── figures ├── DIPGXIII_chr12_demo.png ├── GM12878_K562_chr10_demo.png ├── GM12878_chr10_demo.png ├── K562_chr10_demo.png ├── TADs_chr1.png ├── misc.txt ├── tadlist_demo.png ├── workflow.jpg └── workflow.pdf ├── makefile └── res ├── GM12878_vs_K562_chr1_50M_adjusted_filter.tsv ├── chr1_163500000_165000000.txt ├── images └── side_by_side.pdf ├── reorganized_TADs_GM12878_K562.txt ├── reorganized_TADs_GM12878_K562_filter.txt ├── reorganized_TADs_GM12878_K562_subtypes.txt ├── reorganized_TADs_GM12878_K562_subtypes_up_down.txt └── temp ├── GM12878_vs_K562_chr1_50M_temp.txt └── temp.txt /.DS_Store: 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