Man pages for lisat
Longitudinal Integration Site Analysis Toolkit
| chr_distribution | Plot chromosome distribution of integration sites (IS) |
| CIS | Visualize and analyze network of common integration sites... |
| CIS_overlap | Generate colored GT table for CIS overlap across... |
| Count_regions | Calculate regional distribution percentages of integration... |
| Cumulative_curve | Plot cumulative curve and perform statistical analysis |
| Enhancer_check | Check if integration sites (IS) are located in enhancer... |
| fit_cum_simple | Calculate normalized cumulative sum for top N elements of a... |
| 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... |
| pmd_plot | Generate PMD (Proportional Modular Diversity) Scatter Plot... |
| Promotor_check | Check if integration sites (IS) are located in promoter... |
| Safeharbor_check | Check if integration sites (IS) are located in safe harbor... |
| validate_IS_raw | Validate and standardize integration site (IS) raw data frame |
