Roleswitch

DOI: 10.18129/B9.bioc.Roleswitch    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Roleswitch.

Infer miRNA-mRNA interactions using paired expression data from a single sample

Bioconductor version: 3.12

Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.

Author: Yue Li

Maintainer: Yue Li <yueli at cs.toronto.edu>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("Roleswitch")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Software, miRNA
Version	1.28.0
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	GPL-2
Depends	R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI
Imports
LinkingTo
Suggests	ggplot2
SystemRequirements
Enhances
URL	http://www.cs.utoronto.ca/~yueli/roleswitch.html
Depends On Me
Imports Me	miRLAB
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/Roleswitch
Source Repository (Developer Access)	git clone [email protected]:packages/Roleswitch
Package Short Url	https://bioconductor.org/packages/Roleswitch/
Package Downloads Report	Download Stats