bernoulli_data          Synthetic Bernoulli data
beta_data               Synthetic Beta data
binomial_data           Synthetic Binomial data
boxplot_cluster_expr    Boxplot of clustered expression levels
bpr_cluster_wrap        (DEPRECATED) Cluster methylation profiles
bpr_log_likelihood      Compute observation model log-likelihood
bpr_optimize            (DEPRECATED) Optimize BPR negative log
                        likelihood function
bpr_predict_wrap        (DEPRECATED) Predict gene expression from
                        methylation profiles
BPRMeth                 'BPRMeth': Extracting higher order methylation
                        features
cluster_profiles_mle    Cluster methylation profiles using EM
cluster_profiles_vb     Cluster methylation profiles using VB
create_anno_region      Create annotation regions
create_basis            Create basis objects
create_region_object    Create genomic region data
design_matrix           Generic function for creating design matrices
encode_expr             Processed ENCODE expression data
encode_met              Processed ENCODE methylation data
eval_functions          Evaluate basis functions
gaussian_data           Synthetic Gaussian data
gex_data                Synthetic expression data
impute_bulk_met         Impute/predict bulk methylation states
infer_profiles_gibbs    Infer methylation profiles using Gibbs sampling
infer_profiles_mle      Infer methylation profiles using MLE
infer_profiles_vb       Infer methylation profiles using VB
inner_predict_model_expr
                        (INNER) Predict expression
inner_train_model_expr
                        (INNER) Train expression model from methylation
                        profiles
meth_data               Synthetic bulk methylation data
old_boxplot_cluster_gex
                        (DEPRECATED) Boxplot of clustered expression
                        levels
old_plot_cluster_prof   (DEPRECATED) Plot of clustered methylation
                        profiles
old_plot_fitted_profiles
                        (DEPRECATED) Plot the fit of methylation
                        profiles across a region
partition_bulk_dataset
                        Partition bulk methylation dataset to training
                        and test set
plot_cluster_profiles   Plot clustered methylation profiles across a
                        region
plot_infer_profiles     Plot inferred methylation profiles across a
                        region
plot_predicted_expr     Scatter plot of predicted vs measured gene
                        expression levels
pool_bs_seq_rep         (DEPRECATED) Read and pool replicates from
                        BS-Seq data
predict_expr            Predict gene expression from methylation
                        profiles
preprocess_bs_seq       (DEPRECATED) Pre-process BS-Seq data in any
                        given format
preprocess_final_HTS_data
                        (DEPRECATED) Pre-process final HTS data for
                        downstream analysis
process_haib_caltech_wrap
                        (DEPRECATED) Wrapper for processing ENCODE HAIB
                        and Caltech HTS
read_anno               Read annotation file
read_bs_encode_haib     (DEPRECATED) Read ENCODE HAIB bed formatted
                        BS-Seq file
read_chrom_size         Read genome chromosome sizes file
read_expr               Read expression data file
read_met                Read methylation file
read_rna_encode_caltech
                        (DEPRECATED) Read ENCODE Caltech bed formatted
                        RNA-Seq file
