├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── HTClist2gi_list.R ├── HiCDCPlus.R ├── HiCDCPlus_chr.R ├── HiCDCPlus_parallel.R ├── RcppExports.R ├── add_1D_features.R ├── add_2D_features.R ├── add_hic_counts.R ├── add_hicpro_allvalidpairs_counts.R ├── add_hicpro_matrix_counts.R ├── construct_features.R ├── construct_features_chr.R ├── construct_features_parallel.R ├── expand_1D_features.R ├── extract_hic_eigenvectors.R ├── generate_binned_gi_list.R ├── generate_bintolen_gi_list.R ├── generate_df_gi_list.R ├── get_chr_sizes.R ├── get_chrs.R ├── get_enzyme_cutsites.R ├── gi_list2HTClist.R ├── gi_list_Dthreshold_detect.R ├── gi_list_binsize_detect.R ├── gi_list_read.R ├── gi_list_topdom.R ├── gi_list_validate.R ├── gi_list_write.R ├── hic2icenorm_gi_list.R ├── hicdc2hic.R ├── hicdcdiff.R ├── straw_dump.R └── utils.R ├── README.md ├── inst ├── CITATION ├── NEWS ├── extdata │ ├── GSE131651_NSD2_HIGH_arima_example.hic │ ├── GSE131651_NSD2_LOW_arima_example.hic │ ├── GSE131651_NTKOCTCF_new_example.hic │ ├── GSE131651_TKOCTCF_new_example.hic │ ├── GSE131651_analysis_indices.txt.gz │ ├── GSE63525_HMEC_combined_example.hic │ ├── eigenvector_example.hic │ └── test_bintolen.txt.gz ├── script │ └── extdata_info.txt └── unitTests │ └── test_functions.R ├── man ├── HTClist2gi_list.Rd ├── HiCDCPlus.Rd ├── HiCDCPlus_chr.Rd ├── HiCDCPlus_parallel.Rd ├── add_1D_features.Rd ├── add_2D_features.Rd ├── add_hic_counts.Rd ├── add_hicpro_allvalidpairs_counts.Rd ├── add_hicpro_matrix_counts.Rd ├── construct_features.Rd ├── construct_features_chr.Rd ├── construct_features_parallel.Rd ├── expand_1D_features.Rd ├── extract_hic_eigenvectors.Rd ├── figures │ └── manual.pdf ├── generate_binned_gi_list.Rd ├── generate_bintolen_gi_list.Rd ├── generate_df_gi_list.Rd ├── get_chr_sizes.Rd ├── get_chrs.Rd ├── get_enzyme_cutsites.Rd ├── gi_list2HTClist.Rd ├── gi_list_Dthreshold.detect.Rd ├── gi_list_binsize_detect.Rd ├── gi_list_read.Rd ├── gi_list_topdom.Rd ├── gi_list_validate.Rd ├── gi_list_write.Rd ├── hic2icenorm_gi_list.Rd ├── hicdc2hic.Rd ├── hicdcdiff.Rd ├── straw.Rd └── straw_dump.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── straw.cpp ├── tests └── runTests.R └── vignettes └── HiCDCPlus.Rmd /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mervesa/HiCDCPlus/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mervesa/HiCDCPlus/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mervesa/HiCDCPlus/HEAD/NAMESPACE -------------------------------------------------------------------------------- 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