R: Longitudinal Integration Site Analysis Toolkit

# Longitudinal Integration Site Analysis Toolkit

## Documentation for package ‘lisat’ version 0.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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