Roleswitch: Infer miRNA-mRNA interactions using paired expression data from a single sample
Version 1.14.0

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.

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AuthorYue Li
Bioconductor views miRNA
Date of publicationNone
MaintainerYue Li <yueli@cs.toronto.edu>
LicenseGPL-2
Version1.14.0
URL http://www.cs.utoronto.ca/~yueli/roleswitch.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Roleswitch")

Man pages

diagnosticPlot: Create diagnostic plot for understanding the Roleswitch model...
getSeedMatrix: Get seed-match matrix between defined mRNA and miRNA in an...
roleswitch: Infer miRNA-mRNA interactions using paired expression data...
Roleswitch-package: Infer miRNA-mRNA interactions using paired expression data...
tcga_gbm_testdata: Test data of miRNA and mRNA expression vector.

Functions

Roleswitch Man page
Roleswitch-package Man page
diagnosticPlot Man page Source code
getSeedMatrix Man page Source code
getTranscriptIDwithLongest3UTR Source code
roleswitch Man page Source code
tcga_gbm_testdata Man page

Files

DESCRIPTION
NAMESPACE
R
R/diagnosticPlot.R
R/getSeedMatrix.R
R/roleswitch.R
build
build/vignette.rds
data
data/datalist
data/tcga_gbm_testdata.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/Roleswitch.R
inst/doc/Roleswitch.Rnw
inst/doc/Roleswitch.pdf
man
man/Roleswitch-package.Rd
man/diagnosticPlot.Rd
man/getSeedMatrix.Rd
man/roleswitch.Rd
man/tcga_gbm_testdata.Rd
vignettes
vignettes/Roleswitch.Rnw
vignettes/Roleswitch.bib
Roleswitch documentation built on May 20, 2017, 9:25 p.m.