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 (3.12)

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

Maintainer: Andrea Calabria <calabria.andrea at hsr.it>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 Collision removal functionality
HTML R Script How to use import functions
HTML R Script Using ISAnalytics without RStudio support
HTML R Script Working with aggregate functions
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, Sequencing, SingleCell, Software
Version 1.0.5
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License CC BY 4.0
Depends R (>= 4.0), magrittr
Imports utils, reactable, htmltools, dplyr, readr, tidyr, purrr, rlang, forcats, tibble, BiocParallel, stringr, fs, zip, lubridate, lifecycle, ggplot2, ggrepel, stats, upsetjs, psych, grDevices
LinkingTo
Suggests testthat, covr, knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, roxygen2, vegan
SystemRequirements
Enhances
URL https://github.com//calabrialab/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_1.0.5.tar.gz
Windows Binary ISAnalytics_1.0.5.zip (32- & 64-bit)
macOS 10.13 (High Sierra) ISAnalytics_1.0.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/ISAnalytics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ISAnalytics
Package Short Url https://bioconductor.org/packages/ISAnalytics/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive

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