TargetScore: TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Version 1.14.0

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.

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/software.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("TargetScore")

Getting started

Package overview

Popular man pages

bsxfun.se: bsxfun with single expansion (real Matlab style) (Internal...
getTargetScores: Compute targetScore of an overexpressed human microRNA
logmvgamma: Logarithmic multivariate Gamma function (Internal function)
logsumexp: Compute log(sum(exp(x),dim)) while avoiding numerical...
targetScore: Probabilistic score of genes being the targets of an...
vbgmm: Variational Bayesian Gaussian mixture model (VB-GMM)
vbound: Variational Lower Bound Evaluation
See all...

All man pages Function index File listing

Man pages

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

Functions

TargetScore Man page
TargetScore-package Man page
bsxfun.se Man page Source code
dot.ext Man page Source code
getTargetScores Man page Source code
initialization Man page Source code
logmvgamma Man page Source code
logsumexp Man page Source code
sort_components Man page Source code
targetScore Man page Source code
vbgmm Man page Source code
vbound Man page Source code
vexp Man page Source code
vmax Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/getTargetScores.R
R/targetScore.R
R/vbgmm.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/TargetScore.R
inst/doc/TargetScore.Rnw
inst/doc/TargetScore.pdf
inst/extdata
inst/extdata/realtestdata.RData
man
man/TargetScore-package.Rd
man/bsxfun.se.Rd
man/dot.ext.Rd
man/getTargetScores.Rd
man/initialization.Rd
man/logmvgamma.Rd
man/logsumexp.Rd
man/sort_components.Rd
man/targetScore.Rd
man/vbgmm.Rd
man/vbound.Rd
man/vexp.Rd
man/vmax.Rd
vignettes
vignettes/TargetScore.Rnw
vignettes/TargetScore.bib
TargetScore documentation built on May 20, 2017, 9:24 p.m.

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