IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Since 2010, state-of-the-art bioinformatics tools have allowed researchers to reconstruct and quantify full length transcripts from RNA-seq data. Such genome-wide isoform resolution data has the potential to facilitate both genome-wide analysis of alternative isoform usage and identification of isoform switching. Unfortunately, these types of analyses are still only rarely done and/or reported — in fact, only 11% of articles analyzing RNA-seq data published since 2016 performed any isoform analysis.

To solve these problems we developed IsoformSwitchAnalyzeR. IsoformSwitchAnalyzeR is an easy to use R package which enables statistical identification as well as visualization of isoform switches with predicted functional consequences from RNA-seq data.

Installation

Note that IsoformSwitchAnalyzeR now depends on the pfamAnalyzeR package. This can be installed via this command

if (!requireNamespace("devtools", quietly = TRUE)){
    install.packages("devtools")
}
if (!requireNamespace("pfamAnalyzeR", quietly = TRUE)){
    devtools::install_github("kvittingseerup/pfamAnalyzeR")
}

We highly recommend installing the latest version of IsoformSwitchAnalyzeR from Bioconductor.

This can be done by running the following in an R terminal:

if (!requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
}
BiocManager::install(version='devel')
BiocManager::install("IsoformSwitchAnalyzeR")

Alternatively IsoformSwitchAnalyzeR can be installed from github by running the following in an R terminal:

if (!requireNamespace("devtools", quietly = TRUE)){
    install.packages("devtools")
}
devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE)

Vignette

The vignette contains a lot of information on how to use IsoformSwitchAnalyzeR and what it can be used for. After installation, the vignette can be accessed from the R console by typing:

browseVignettes("IsoformSwitchAnalyzeR")

Alternatively, it can be accessed online (through Bioconductor) here