scanMiR

DOI: 10.18129/B9.bioc.scanMiR    

scanMiR

Bioconductor version: Release (3.14)

A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

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

Maintainer: Fridolin Gross <fridolin.gross at hest.ethz.ch>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("scanMiR")

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("scanMiR")

 

HTML	R Script	1_scanning
HTML	R Script	2_Kdmodels
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, 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	Biostrings, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, gridExtra, seqLogo
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	scanMiRApp, scanMiRData
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scanMiR_1.0.0.tar.gz
Windows Binary	scanMiR_1.0.0.zip
macOS 10.13 (High Sierra)	scanMiR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scanMiR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scanMiR
Package Short Url	https://bioconductor.org/packages/scanMiR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive