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scanMiRApp

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

scanMiR shiny application


Bioconductor version: Development (3.19)

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 hest.ethz.ch>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scanMiRApp")

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

Documentation

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

browseVignettes("scanMiRApp")
IndexedFst HTML R Script
scanMiRApp HTML R Script
Reference Manual PDF

Details

biocViews GUI, SequenceMatching, ShinyApps, Software, miRNA
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
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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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Package Archives

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

Source Package scanMiRApp_1.9.0.tar.gz
Windows Binary scanMiRApp_1.9.0.zip
macOS Binary (x86_64) scanMiRApp_1.9.0.tgz
macOS Binary (arm64) scanMiRApp_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scanMiRApp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scanMiRApp
Bioc Package Browser https://code.bioconductor.org/browse/scanMiRApp/
Package Short Url https://bioconductor.org/packages/scanMiRApp/
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