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ISAnalytics

This is the development version of ISAnalytics; for the stable release version, see ISAnalytics.

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


Bioconductor version: Development (3.19)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ISAnalytics")

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

Documentation

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

browseVignettes("ISAnalytics")
ISAnalytics HTML R Script
workflow_start HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, Sequencing, SingleCell, Software
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License CC BY 4.0
Depends R (>= 4.3)
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
System Requirements
URL https://calabrialab.github.io/ISAnalytics https://github.com//calabrialab/isanalytics https://calabrialab.github.io/ISAnalytics/
Bug Reports https://github.com/calabrialab/ISAnalytics/issues
See More
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
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Package Archives

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

Source Package ISAnalytics_1.13.0.tar.gz
Windows Binary ISAnalytics_1.13.0.zip
macOS Binary (x86_64) ISAnalytics_1.13.0.tgz
macOS Binary (arm64) ISAnalytics_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ISAnalytics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ISAnalytics
Bioc Package Browser https://code.bioconductor.org/browse/ISAnalytics/
Package Short Url https://bioconductor.org/packages/ISAnalytics/
Package Downloads Report Download Stats