Package: ISAnalytics
Title: Analyze gene therapy vector insertion sites data identified from
        genomics next generation sequencing reads for clonal tracking
        studies
Version: 1.22.0
Date: 2025-07-21
Authors@R: c(
  person(given = "Francesco",
         family = "Gazzo",
         role = c("cre"),
         email = "gazzo.francesco@hsr.it",
         comment = c(ORCID = "0009-0000-4626-1386")),
  person(given = "Giulia",
         family = "Pais",
         role = c("aut"),
         email = "giuliapais1@gmail.com",
         comment = c(ORCID = "0009-0005-5621-4803")),
  person(given = "Andrea",
         family = "Calabria",
         role = c("aut"),
         email = "calabria.andrea@hsr.it"),
  person(given = "Giulio",
         family = "Spinozzi",
         role = c("aut"),
         email = "spinozzi.giulio@hsr.it"))
Description: In gene therapy, stem cells are modified using viral
        vectors to deliver the therapeutic transgene and replace
        functional properties since the genetic modification is stable
        and inherited in all cell progeny. The retrieval and mapping of
        the sequences flanking the virus-host DNA junctions allows the
        identification of insertion sites (IS), essential for
        monitoring the evolution of genetically modified cells in vivo.
        A comprehensive toolkit for the analysis of IS is required to
        foster clonal trackign studies and supporting the assessment of
        safety and long term efficacy in vivo. This package is aimed at
        (1) supporting automation of IS workflow, (2) performing base
        and advance analysis for IS tracking (clonal abundance, clonal
        expansions and statistics for insertional mutagenesis, etc.),
        (3) providing basic biology insights of transduced stem cells
        in vivo.
License: CC BY 4.0
URL: https://calabrialab.github.io/ISAnalytics,
        https://github.com//calabrialab/isanalytics,
        https://calabrialab.github.io/ISAnalytics/
BugReports: https://github.com/calabrialab/ISAnalytics/issues
biocViews: BiomedicalInformatics, Sequencing, SingleCell, CellBiology,
        FunctionalGenomics, DataImport
Depends: R (>= 4.5)
Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
        lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
        grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
        vegan, data.table, DT
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
        roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra,
        R.utils, RefManageR, flexdashboard, circlize, plotly, gtools,
        eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr,
        future, doFuture, foreach, psych, Rcapture
VignetteBuilder: knitr
RdMacros: lifecycle
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:53:33 UTC
RemoteUrl: https://github.com/bioc/ISAnalytics
RemoteRef: RELEASE_3_23
RemoteSha: e6dd0369ad3afa568f83608016d57f60e06ca018
NeedsCompilation: no
Packaged: 2026-04-29 22:29:02 UTC; root
Author: Francesco Gazzo [cre] (ORCID: <https://orcid.org/0009-0000-4626-1386>),
  Giulia Pais [aut] (ORCID: <https://orcid.org/0009-0005-5621-4803>),
  Andrea Calabria [aut],
  Giulio Spinozzi [aut]
Maintainer: Francesco Gazzo <gazzo.francesco@hsr.it>
Built: R 4.6.0; ; 2026-04-29 22:30:56 UTC; windows
