QCmetric.scopeDemo      Pre-stored QCmetric data for demonstration
                        purposes
Y_sim                   A read count matrix in the toy dataset
coverageObj.scopeDemo   Pre-stored coverageObj.scope data for
                        demonstration purposes
get_bam_bed             Get bam file directories, sample names, and
                        whole genomic bins
get_coverage_scDNA      Get read coverage from single-cell DNA
                        sequencing
get_gc                  Compute GC content
get_gini                Compute Gini coefficients for single cells
get_mapp                Compute mappability
get_samp_QC             Get QC metrics for single cells
iCN_sim                 A post cross-sample segmentation integer copy
                        number matrix returned by SCOPE in the demo
initialize_ploidy       Ploidy pre-initialization
initialize_ploidy_group
                        Group-wise ploidy pre-initialization
normObj.scopeDemo       Pre-stored normObj.scope data for demonstration
                        purposes
normalize_codex2_ns_noK
                        Normalization of read depth without latent
                        factors under the case-control setting
normalize_scope         Normalization of read depth with latent factors
                        using Expectation-Maximization algorithm under
                        the case-control setting
normalize_scope_foreach
                        Normalization of read depth with latent factors
                        using Expectation-Maximization algorithm under
                        the case-control setting in parallel
normalize_scope_group   Group-wise normalization of read depth with
                        latent factors using Expectation-Maximization
                        algorithm and shared clonal memberships
perform_qc              Quality control for cells and bins
plot_EM_fit             Visualize EM fitting for each cell.
plot_iCN                Plot post-segmentation copy number profiles of
                        integer values
ref.scopeDemo           Pre-stored 500kb-size reference genome for
                        demonstration purposes
ref_sim                 A reference genome in the toy dataset
segment_CBScs           Cross-sample segmentation
