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.
BiocManager::install("ETHZ-INS/scanMiR")
# 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:
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). For
more information, see our paper.
To learn more about the functionalities, see the package's
vignettes.
To obtain predicted KdModels for all mouse, human and rat miRbase miRNAs, see the
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 package.