ELViS                   ELViS : An R Package for Estimating Copy Number
                        Levels of Viral Genome Segments Using
                        Base-Resolution Read Depth Profile.
ELViS_toy_run_result    ELViS Toy Example - Run Result
coord_to_grng           Convert coordinate string to grng object
coord_to_lst            Convert coordinate string to list of chr,start
                        and end
depth_hist              Sample filtering threshold examination plot.
filt_samples            Filtering samples based on summary statistic
gene_cn_heatmaps        Gene Copy Number Heatmap
get_depth_matrix        Generate a read depth matrix of positions x
                        samples from input BAM files list
get_new_baseline        Get new baselines according to criteria user
                        designates
integrative_heatmap     Plot heatmaps based on simple integrative
                        clustering of multiple matrices
mtrx_samtools_reticulate
                        ELViS Toy Example - Base-Resolution Raw Read
                        Depth
norm_fun                Normalization - scaling by certain quantile
plot_pileUp_multisample
                        Get a list of pile-up plots over multiple
                        samples
run_ELViS               Run ELViS using input raw depth matrix
total_aligned_base__host_and_virus
                        ELViS Toy Example - Total Aligned Base
toy_example             ELViS Toy Example - Metadata
