scanMiRApp

scanMiR shiny application

Bioconductor version: Release (3.17)

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 "4.3") and enter:

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

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	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 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
Linking To
Suggests	knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scanMiRApp_1.6.0.tar.gz
Windows Binary	scanMiRApp_1.6.0.zip
macOS Binary (x86_64)	scanMiRApp_1.6.0.tgz
macOS Binary (arm64)	scanMiRApp_1.6.0.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/
Package Downloads Report	Download Stats