TargetScore
This is the released version of TargetScore; for the devel version, see TargetScore.
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Bioconductor version: Release (3.23)
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>
citation("TargetScore")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software, miRNA |
| Version | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL-2 |
| Depends | pracma, Matrix |
| Imports | |
| System Requirements | |
| URL | http://www.cs.utoronto.ca/~yueli/software.html |
See More
| Suggests | TargetScoreData, gplots, Biobase, GEOquery |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | TargetScoreData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TargetScore_1.50.0.tar.gz |
| Windows Binary (x86_64) | TargetScore_1.50.0.zip |
| macOS Binary (big-sur-x86_64) | TargetScore_1.50.0.tgz |
| macOS Binary (sonoma-arm64) | TargetScore_1.50.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TargetScore |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TargetScore |
| Bioc Package Browser | https://code.bioconductor.org/browse/TargetScore/ |
| Package Short Url | https://bioconductor.org/packages/TargetScore/ |
| Package Downloads Report | Download Stats |