A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
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A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
library(scanMiR)
data("SampleTranscript")
data("SampleKdModel")
# Scan for matches using a KdModel
matches <- findSeedMatches(SampleTranscript, SampleKdModel, verbose = FALSE)
# View target alignment
viewTargetAlignment(matches[1], SampleKdModel, SampleTranscript)
# Aggregate matches
agg_matches <- aggregateMatches(matches)
Input: A transcript sequence (DNAStringSet or character) and a miRNA KdModel; Output: A GRanges object of matches and a data.frame of aggregated repression values.
DNAStringSet) for miRNA binding sites using a seed sequence, full miRNA sequence, or a KdModel using findSeedMatches.assignKdType.viewTargetAlignment or plot KdModel affinities using plotKdModel.aggregateMatches.DESeq2 or edgeR).KdModel / KdModelList objects.DNAStringSet (optionally with ORF.length metadata column).TRUE/FALSE): Controls progress reporting during scanning in findSeedMatches.FALSE): Restricts the scan to canonical miRNA binding sites when using a KdModel."GRanges"): Specifies the return format of findSeedMatches (e.g., "GRanges", "data.frame", or "aggregated").0): Treats matches within the first shadow positions of the UTR as if they were in the ORF.7): Minimum distance between matches of the same miRNA; only the highest affinity match is kept."seeds"): Specifies what to plot in plotKdModel (e.g., "seeds").ORF.length as a metadata column in the input DNAStringSet to distinguish between matches in the ORF and 3'UTR regions.onlyCanonical = TRUE in findSeedMatches if you want to exclude low-affinity non-canonical binding sites.aggregateMatches to compute the predicted repression of transcripts based on the biochemical model of occupancy.BiocParallel parameter (e.g., BP = MulticoreParam()) to findSeedMatches.n_seeds parameter or set useTmpFiles = TRUE.targetscan: For standard TargetScan-based miRNA target predictions.mirbase: For retrieving miRNA sequences and annotations.No reviews yet. Tell others what you thought.
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