Roleswitch
This package is for version 3.9 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: 3.9
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>
citation("Roleswitch")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Roleswitch")
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("Roleswitch")| Roleswitch | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software, miRNA |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI |
| Imports | |
| System Requirements | |
| URL | http://www.cs.utoronto.ca/~yueli/roleswitch.html |
See More
| Suggests | ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | miRLAB |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Roleswitch_1.22.0.tar.gz |
| Windows Binary | Roleswitch_1.22.0.zip |
| Mac OS X 10.11 (El Capitan) | Roleswitch_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Roleswitch |
| Source Repository (Developer Access) | git clone [email protected]:packages/Roleswitch |
| Bioc Package Browser | https://code.bioconductor.org/browse/Roleswitch/ |
| Package Short Url | https://bioconductor.org/packages/Roleswitch/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |