Bioconductor Code: scanMiR (original) (raw)

[\](https://doi.org/10.1093/bioinformatics/btac110) [\](https://github.com/ETHZ-INS/scanMiR/actions) # scanMiR `scanMiR` is a bioconductor set of tools for working with miRNA affinity models (KdModels), enabling efficient and flexible scanning for miRNA binding sites and prediction of target repression. This repository details the R package; for the web interface [click here](http://ethz-ins.org/scanMiR/).
## Getting started ### Installation ```{r} BiocManager::install("ETHZ-INS/scanMiR") ``` ### Basic example usage ```{r} # accepts miRNA target seeds: findSeedMatches(seqs, seeds="AAACCAC") # full miRNA sequences: findSeedMatches(seqs, seeds="UUAAUGCUAAUCGUGAUAGGGGUU") # or KdModels: findSeedMatches(seqs, seeds=model) ``` ``` GRanges object with 43 ranges and 4 metadata columns: seqnames ranges strand | p3.score type log_kd note | [1] seq2 2687-2694 * | 4 7mer-a1 -3607 - [2] seq2 2358-2365 * | 0 6mer -2341 - [3] seq2 2550-2557 * | 0 6mer-m8 -986 - [4] seq2 1642-1649 * | 0 non-canonical -952 - [5] seq2 920-927 * | 0 non-canonical -847 - ... ... ... ... . ... ... ... ... ``` The putative 3' binding of each match can also be visualized: ```{r} viewTargetAlignment(matches[1], miRNA=model, seqs=seqs) ``` ``` miRNA 3'-UUGGGGAUAGUGCUA---AUCGUAAUU-5' ||||| ||||||- target 5'-...NUAUAGACGAGUGACCUACGAUAUGCCGCAUUAAUU...-3' ```


`scanMiR` can predict TDMD and circRNA slicing sites, and aggregate sites to predict repression based on the biochemical model from [McGeary, Lin et al. (2019)](https://dx.doi.org/10.1126/science.aav1741). For more information, see our [paper](https://doi.org/10.1093/bioinformatics/btac110). To learn more about the functionalities, see the package's [vignettes](https://www.bioconductor.org/packages/devel/bioc/vignettes/scanMiR/inst/doc/scanning.html). To obtain predicted `KdModels` for all mouse, human and rat miRbase miRNAs, see the [scanMiRData](https://github.com/ETHZ-INS/scanMiRData) pacakge. For convenient wrappers connecting to AnnotationHub, fast out-of memory access to large collections, or a web interface to scanMiR, see the [scanMiRApp](https://github.com/ETHZ-INS/scanMiRApp) package.