TargetScore

DOI: 10.18129/B9.bioc.TargetScore    

TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information

Bioconductor version: Release (3.15)

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

Author: Yue Li

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("TargetScore")

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("TargetScore")

 

PDF	R Script	TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, miRNA
Version	1.34.0
In Bioconductor since	BioC 2.13 (R-3.0) (9 years)
License	GPL-2
Depends	pracma, Matrix
Imports
LinkingTo
Suggests	TargetScoreData, gplots, Biobase, GEOquery
SystemRequirements
Enhances
URL	http://www.cs.utoronto.ca/~yueli/software.html
Depends On Me
Imports Me
Suggests Me	TargetScoreData
Links To Me
Build Report

Package Archives

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

Source Package	TargetScore_1.34.0.tar.gz
Windows Binary	TargetScore_1.34.0.zip
macOS Binary (x86_64)	TargetScore_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TargetScore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TargetScore
Package Short Url	https://bioconductor.org/packages/TargetScore/
Package Downloads Report	Download Stats