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