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.


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)){
BiocManager::install("IsoformSwitchAnalyzeR", version = "3.9")

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

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


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:


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

kvittingseerup/IsoformSwitchAnalyzeR documentation built on Oct. 20, 2019, 1:41 p.m.