CIS                     Visualize and analyze network of common
                        integration sites (CIS)
CIS_overlap             Generate colored GT table for CIS overlap
                        across samples/timepoints
Count_regions           Calculate regional distribution percentages of
                        integration sites (IS)
Cumulative_curve        Plot cumulative curve and perform statistical
                        analysis
Enhancer_check          Check if integration sites (IS) are located in
                        enhancer regions
IS_treemap              Generate treemap of integration site clone
                        contribution
Linked_timepoints       Generate Linked Timepoint Sankey + Stacked Bar
                        Chart
Promotor_check          Check if integration sites (IS) are located in
                        promoter regions
Safeharbor_check        Check if integration sites (IS) are located in
                        safe harbor regions
chr_distribution        Plot chromosome distribution of integration
                        sites (IS)
fit_cum_simple          Calculate normalized cumulative sum for top N
                        elements of a numeric vector
get_feature             Annotate integration site (IS) data with
                        genomic features
ideogram_plot           Plot chromosome ideogram with integration site
                        annotations
is_in_AE_gene           Plot AE-associated gene clone contribution
is_in_CG_gene           Plot Cancer-associated gene clone contribution
is_in_immune_gene       Plot Immune-associated gene clone contribution
plot_regions            Plot Region-wise Donut Charts
plot_richness_evenness
                        Plot Richness & Evenness Dual Y-Axis Line Chart
pmd_analysis            Calculate PMD (Proportional Modular Diversity)
                        for integration site data
pmd_plot                Generate PMD (Proportional Modular Diversity)
                        Scatter Plot with Inset Legend
validate_IS_raw         Validate and standardize integration site (IS)
                        raw data frame
