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>

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

Installation

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

if (!requireNamespace("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

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