Longitudinal Integration Site Analysis Toolkit

Documentation for package ‘lisat’ version 0.1.2

chr_distribution	Plot chromosome distribution of integration sites (IS)
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
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
IS_treemap	Generate treemap of integration site clone contribution
Linked_timepoints	Generate Linked Timepoint Sankey + Stacked Bar Chart
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
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
validate_IS_raw	Validate and standardize integration site (IS) raw data frame