Package: lisat 0.1.2

Shuai Ni

lisat: Longitudinal Integration Site Analysis Toolkit

A comprehensive toolkit for the analysis of longitudinal integration site data, including data cleaning, quality control, statistical modeling, and visualization. It streamlines the entire workflow of integration site analysis, supports simple input formats, and provides user-friendly functions for researchers in virus integration site analysis. Ni et al. (2025) <doi:10.64898/2025.12.20.695672>.

Authors:Shuai Ni [aut, cre]

lisat_0.1.2.tar.gz
lisat_0.1.2.tar.gz(r-4.7-any)lisat_0.1.2.tar.gz(r-4.6-any)
lisat_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
lisat/json (API)

# Install 'lisat' in R:

install.packages('lisat', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 400 downloads 21 exports 89 dependencies

Last updated from:30c7ca7c3e. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	464
source / vignettes	OK	409
linux-release-x86_64	OK	395
wasm-release	OK	234

Exports:chr_distribution CIS CIS_overlap Count_regions Cumulative_curve Enhancer_check fit_cum_simple get_feature ideogram_plot is_in_AE_gene is_in_CG_gene is_in_immune_gene IS_treemap Linked_timepoints plot_regions plot_richness_evenness pmd_analysis pmd_plot Promotor_check Safeharbor_check validate_IS_raw

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob broom cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray dplyr farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XML XVector yaml

Introduction to LISAT

Rendered fromlisat-intro.Rmdusingknitr::rmarkdown

Last update: 2026-03-27
Started: 2026-03-27

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

Package: lisat 0.1.2

lisat: Longitudinal Integration Site Analysis Toolkit

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)