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

knitr::opts_chunk$set(echo = TRUE)

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)

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