├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── BPRMeth_package.R ├── RcppExports.R ├── basis_functions.R ├── cluster_profiles_mle.R ├── cluster_profiles_vb.R ├── data.R ├── deprecated_functions.R ├── deprecated_process_functions.R ├── design_matrix.R ├── infer_profiles_gibbs.R ├── infer_profiles_mle.R ├── infer_profiles_vb.R ├── model_log_likelihood.R ├── plotting_functions.R ├── predict_expr.R ├── process_data.R └── utils.R ├── README.md ├── data-raw ├── create_encode_data.R └── create_synth_data.R ├── data ├── bernoulli_data.rda ├── beta_data.rda ├── binomial_data.rda ├── encode_expr.rda ├── encode_met.rda ├── gaussian_data.rda ├── gex_data.rda └── meth_data.rda ├── inst ├── CITATION ├── NEWS.Rd ├── extdata │ ├── dummy_anno.bed │ ├── dummy_expr.bed │ ├── dummy_met.bed │ ├── hg19.chr.sizes │ ├── rnaseq.bed │ └── rrbs.bed └── figures │ ├── bprmeth-workflow.png │ ├── model.png │ └── workflow.png ├── man ├── BPRMeth.Rd ├── bernoulli_data.Rd ├── beta_data.Rd ├── binomial_data.Rd ├── boxplot_cluster_expr.Rd ├── bpr_cluster_wrap.Rd ├── bpr_optimize.Rd ├── bpr_predict_wrap.Rd ├── cluster_profiles_mle.Rd ├── cluster_profiles_vb.Rd ├── create_anno_region.Rd ├── create_basis.Rd ├── create_region_object.Rd ├── design_matrix.Rd ├── encode_expr.Rd ├── encode_met.Rd ├── eval_functions.Rd ├── gaussian_data.Rd ├── gex_data.Rd ├── impute_bulk_met.Rd ├── infer_profiles_gibbs.Rd ├── infer_profiles_mle.Rd ├── infer_profiles_vb.Rd ├── inner_predict_model_expr.Rd ├── inner_train_model_expr.Rd ├── meth_data.Rd ├── model_log_likelihood.Rd ├── old_boxplot_cluster_gex.Rd ├── old_plot_cluster_prof.Rd ├── old_plot_fitted_profiles.Rd ├── partition_bulk_dataset.Rd ├── plot_cluster_profiles.Rd ├── plot_infer_profiles.Rd ├── plot_predicted_expr.Rd ├── pool_bs_seq_rep.Rd ├── predict_expr.Rd ├── preprocess_bs_seq.Rd ├── preprocess_final_HTS_data.Rd ├── process_haib_caltech_wrap.Rd ├── read_anno.Rd ├── read_bs_encode_haib.Rd ├── read_chrom_size.Rd ├── 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