DOI: 10.18129/B9.bioc.scanMiRApp  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scanMiRApp.

scanMiR shiny application

Bioconductor version: 3.16

A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

Author: Pierre-Luc Germain [cre, aut] , Michael Soutschek [aut], Fridolin Gross [ctb]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at>

Citation (from within R, enter citation("scanMiRApp")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script IndexedFst
HTML R Script scanMiRApp
PDF   Reference Manual


biocViews GUI, SequenceMatching, ShinyApps, Software, miRNA
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Depends R (>= 4.0)
Imports AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiR, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, waiter
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6
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Source Package scanMiRApp_1.4.0.tar.gz
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macOS Binary (x86_64) scanMiRApp_1.4.0.tgz
macOS Binary (arm64) scanMiRApp_1.4.0.tgz
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