[](https://doi.org/10.1093/bioinformatics/btac110)
[](https://github.com/ETHZ-INS/scanMiR/actions)
<img align="right" style="margin-left: 20px; margin-bottom: 10px;" src="inst/docs/sticker.svg"/>
# 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/).
<br/>
## 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
<Rle> <IRanges> <Rle> | <integer> <factor> <integer> <Rle>
[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'
```
<br/><br/><br/>
`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.
