index.md

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

ISAnalytics

ISAnalytics is an R package developed to analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies.

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.

Installation and options

ISAnalytics can be installed quickly in different ways:

• You can install it via Bioconductor
• You can install it via GitHub using the package devtools

There are always 2 versions of the package active:

• RELEASE is the latest stable version
• DEVEL is the development version, it is the most up-to-date version where all new features are introduced

Installation from bioconductor

RELEASE version:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ISAnalytics")

DEVEL version:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ISAnalytics")

Installation from GitHub

RELEASE:

if (!require(devtools)) {
  install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
                         ref = "RELEASE_3_17",
                         dependencies = TRUE,
                         build_vignettes = TRUE)

DEVEL:

if (!require(devtools)) {
  install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
                         ref = "devel",
                         dependencies = TRUE,
                         build_vignettes = TRUE)

Setting options

ISAnalytics has a verbose option that allows some functions to print additional information to the console while they’re executing. To disable this feature do:

# DISABLE
options("ISAnalytics.verbose" = FALSE)
# ENABLE
options("ISAnalytics.verbose" = TRUE)

Some functions also produce report in a user-friendly HTML format, to set this feature:

# DISABLE HTML REPORTS
options("ISAnalytics.reports" = FALSE)
# ENABLE HTML REPORTS
options("ISAnalytics.reports" = TRUE)

Getting help

For help please contact the maintainer of the package or open an issue on GitHub.

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.