Package: TargetScore 1.51.0

Yue Li

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

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.

Authors:Yue Li

TargetScore_1.51.0.tar.gz
TargetScore_1.51.0.zip(r-4.7)TargetScore_1.51.0.zip(r-4.6)TargetScore_1.51.0.zip(r-4.5)
TargetScore_1.51.0.tgz(r-4.6-any)TargetScore_1.51.0.tgz(r-4.5-any)
TargetScore_1.51.0.tar.gz(r-4.7-any)TargetScore_1.51.0.tar.gz(r-4.6-any)
TargetScore_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TargetScore/json (API)

# Install 'TargetScore' in R:

install.packages('TargetScore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:TargetScore-1.51.0(bioc 3.24)TargetScore-1.50.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

mirna

4.00 score 9 scripts 5 mentions 12 exports 3 dependencies

Last updated from:ff78e08775. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	155
linux-devel-x86_64	NOTE	172
source / vignettes	OK	265
linux-release-x86_64	NOTE	169
macos-release-arm64	NOTE	99
macos-oldrel-arm64	NOTE	122
windows-devel	NOTE	100
windows-release	NOTE	99
windows-oldrel	NOTE	96
wasm-release	OK	123

Exports:bsxfun.se dot.ext getTargetScores initialization logmvgamma logsumexp sort_components targetScore vbgmm vbound vexp vmax

Dependencies:lattice Matrix pracma

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

Rendered fromTargetScore.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information	TargetScore-package TargetScore
bsxfun with single expansion (real Matlab style) (Internal function)	bsxfun.se
Elementwise dot product (modified dot function) (Internal function)	dot.ext
Compute targetScore of an overexpressed human microRNA	getTargetScores
Initialization of latent variable assignments (responsibility) of the VB-GMM (Internal function)	initialization
Logarithmic multivariate Gamma function (Internal function)	logmvgamma
Compute log(sum(exp(x),dim)) while avoiding numerical underflow (Internal function)	logsumexp
Sort mixture components in increasing order of averaged means (Internal function)	sort_components
Probabilistic score of genes being the targets of an overexpressed microRNA	targetScore
Variational Bayesian Gaussian mixture model (VB-GMM)	vbgmm
Variational Lower Bound Evaluation	vbound
Variational-Expectation in VB-EM (Internal function)	vexp
Variational-Maximimization in VB-EM (Internal function)	vmax

Package: TargetScore 1.51.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)