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scanMiR

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

scanMiR


Bioconductor version: Development (3.19)

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 [cre, aut] , Michael Soutschek [aut], Fridolin Gross [aut]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>

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

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("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")
1_scanning HTML R Script
2_Kdmodels HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, SequenceMatching, Software, miRNA
Version 1.9.3
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.0)
Imports Biostrings, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me scanMiRApp, scanMiRData
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scanMiR_1.9.3.tar.gz
Windows Binary scanMiR_1.9.3.zip
macOS Binary (x86_64) scanMiR_1.9.3.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scanMiR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scanMiR
Bioc Package Browser https://code.bioconductor.org/browse/scanMiR/
Package Short Url https://bioconductor.org/packages/scanMiR/
Package Downloads Report Download Stats