Roleswitch

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("Roleswitch")

To cite this package in a publication, start R and enter:

    citation("Roleswitch")

Documentation

PDF R Script Roleswitch
PDF   Reference Manual

Details

biocViews Software, miRNA
Version 1.3.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2
Depends R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI
Imports
Suggests ggplot2
System Requirements
URL http://www.cs.utoronto.ca/~yueli/roleswitch.html
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source Roleswitch_1.3.0.tar.gz
Windows Binary Roleswitch_1.3.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Roleswitch_1.3.0.tgz
Mac OS X 10.9 (Mavericks)
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