<img align="right" style="margin-left: 25px; margin-bottom: 30px;" src="https://raw.githubusercontent.com/ETHZ-INS/scanMiR/master/inst/docs/sticker.svg"/> # scanMiRApp `scanMiRApp` is a companion package to <a href="https://github.com/ETHZ-INS/scanMiR">scanMiR</a>. It contains: * A shiny interface to the <a href="https://github.com/ETHZ-INS/scanMiR">scanMiR</a> 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 <a href="vignettes/IndexedFST.Rmd">`IndexedFst`</a> 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](https://ethz-ins.org/scanMiR/) for a live version of the app. For more information, see the package's [vignettes](vignettes/) and the [preprint](https://doi.org/10.1101/2021.06.16.448293). ## Installation First ensure that <a href="https://github.com/ETHZ-INS/scanMiR">scanMiR</a> and <a href="https://github.com/ETHZ-INS/scanMiRData">scanMiRData</a> are installed, then install with: ```{r} BiocManager::install("ETHZ-INS/scanMiRApp") ```