├── .DS_Store ├── .gitattributes ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── CALDER_hierarchy.R ├── CALDER_main.R ├── HRG_MLE_each_compartment_fun.R ├── HighResolution2Low.R ├── LikelihoodRatioTest_fun.R ├── RcppExports.R ├── bisecting_kmeans.R ├── call_domains.R ├── compartment_PCA.R ├── compartment_data_generation_fun.R ├── general_functions.R ├── generate_compartments_bed_fun.R ├── post_processing_nested_domains.R ├── prunning.R └── zigzag_nested_domain.R ├── README.md ├── Read-and-delete-me ├── img ├── CALDER_methods.png ├── Hela_chr11_and_RWPE1_chr9_pq.png └── IGV_results.png ├── inst ├── .DS_Store └── extdata │ ├── TxDb.Hsapiens.UCSC.hg19.knownGene.rds │ ├── TxDb.Mmusculus.UCSC.mm9.knownGene.rds │ ├── mat_chr22_10kb_ob.txt.gz │ └── mat_mm9_chr1_100kb_ob.txt.gz ├── man ├── .Rapp.history └── CALDER-package.Rd └── src ├── .DS_Store ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── matrix_multiplication_fun.cpp └── zigzag_loglik_ancestors_v4.5.cpp 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