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This is the development version of scanMiRApp; for the stable release version, see scanMiRApp.

scanMiR shiny application

Bioconductor version: Development (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

IndexedFst HTML R Script
scanMiRApp HTML R Script
Reference Manual PDF


biocViews GUI, SequenceMatching, ShinyApps, Software, miRNA
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.0), scanMiR
Imports AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter
System Requirements
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Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scanMiRApp_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64) scanMiRApp_1.11.0.tgz
macOS Binary (arm64) scanMiRApp_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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