ISAnalytics

DOI: 10.18129/B9.bioc.ISAnalytics  

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

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	BiomedicalInformatics, Sequencing, SingleCell, Software
Version	1.10.2
In Bioconductor since	BioC 3.12 (R-4.0) (3 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://calabrialab.github.io/ISAnalytics https://github.com//calabrialab/isanalytics https://calabrialab.github.io/ISAnalytics/
BugReports	https://github.com/calabrialab/ISAnalytics/issues
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_1.10.2.tar.gz
Windows Binary	ISAnalytics_1.10.2.zip (64-bit only)
macOS Binary (x86_64)	ISAnalytics_1.10.2.tgz
macOS Binary (arm64)	ISAnalytics_1.10.2.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
Old Source Packages for BioC 3.17	Source Archive