DOI: 10.18129/B9.bioc.ISAnalytics  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ISAnalytics.

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Bioconductor version: 3.16

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.

Author: Giulia Pais [aut, cre] , Andrea Calabria [aut], Giulio Spinozzi [aut]

Maintainer: Giulia Pais <giuliapais1 at>

Citation (from within R, enter citation("ISAnalytics")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script ISAnalytics
HTML R Script workflow_start
PDF   Reference Manual
Text   NEWS


biocViews BiomedicalInformatics, Sequencing, SingleCell, Software
Version 1.8.3
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License CC BY 4.0
Depends R (>= 4.2)
Imports utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT
Suggests testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ISAnalytics_1.8.3.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ISAnalytics_1.8.3.tgz
macOS Binary (arm64) ISAnalytics_1.8.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: