scanMiRApp

scanMiRApp is a companion package to scanMiR. It contains:

• A shiny interface to the scanMiR package, enabling the scanning of transcripts (or custom sequences) for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data.
• The ScanMiRAnno class, which encapsulates all the annotation information necessary for the app/wrappers in this package for a given species.
• The IndexedFst class for fast indexed reading of large GenomicRanges or data.frames; this is used to enable fast random access to pre-compiled scans and aggregations without having to load them in memory.
• A number of convenience wrappers to scanMiR functions, for tasks like scanning or visualizing sites on the UTR of a given transcript, running transcriptome-wide scans, or finding enriched miRNA-target pairs.

Click here for a live version of the app. For more information, see the package's vignettes and the preprint.

Installation

First ensure that scanMiR and scanMiRData are installed, then install with:

BiocManager::install("ETHZ-INS/scanMiRApp")