IsoformSwitchAnalyzeR - An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences from 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 recommend installing the latest version of IsoformSwitchAnalyzeR from Bioconductor (where instructions also can be found): https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html
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: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html