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>.

Version:	0.1.2
Depends:	R (≥ 3.5)
Imports:	GenomicRanges (≥ 1.50.0), IRanges (≥ 2.32.0), tidyr (≥ 1.3.0), dplyr (≥ 1.1.4), AnnotationDbi (≥ 1.50.0), S4Vectors (≥ 0.32.0), GenomicFeatures (≥ 1.50.0), magrittr, ggplot2, purrr, broom
Suggests:	TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, knitr, rmarkdown, grid, gt (≥ 0.9.0), gtable (≥ 0.3.6), this.path (≥ 2.0.0), plotrix (≥ 3.8-2), scales (≥ 1.2.0), writexl (≥ 1.4.0), ggrepel (≥ 0.9.4), ggpubr (≥ 0.6.0), viridisLite (≥ 0.4.2), RIdeogram (≥ 0.2.2), patchwork (≥ 1.1.3), RColorBrewer (≥ 1.1-3), colorspace, treemapify, igraph, visNetwork, Cairo (≥ 1.6-1), testthat (≥ 3.0.0)
Published:	2026-03-27
DOI:	10.32614/CRAN.package.lisat
Author:	Shuai Ni [aut, cre]
Maintainer:	Shuai Ni <Nishuai at wakerbio.com>
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README
CRAN checks:	lisat results

Documentation:

Reference manual:	lisat.html , lisat.pdf
Vignettes:	Introduction to LISAT (source, R code)

Downloads:

Package source:	lisat_0.1.2.tar.gz
Windows binaries:	r-devel: lisat_0.1.2.zip, r-release: lisat_0.1.2.zip, r-oldrel: lisat_0.1.2.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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