scanMiRApp

DOI: 10.18129/B9.bioc.scanMiRApp    

scanMiR shiny application

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script IndexedFst
HTML R Script scanMiRApp
PDF   Reference Manual

Details

biocViews GUI, SequenceMatching, Software, miRNA
Version 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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, stats, utils, waiter
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6
SystemRequirements
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_1.0.0.tar.gz
Windows Binary scanMiRApp_1.0.0.zip
macOS 10.13 (High Sierra) scanMiRApp_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scanMiRApp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scanMiRApp
Package Short Url https://bioconductor.org/packages/scanMiRApp/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: