To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RIVER")
In most cases, you don't need to download the package archive at all.
RIVER
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R package for RIVER (RNA-Informed Variant Effect on Regulation)
Bioconductor version: Release (3.5)
An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.
Author: Yungil Kim [aut, cre], Alexis Battle [aut]
Maintainer: Yungil Kim <ipw012 at gmail.com>
Citation (from within R,
enter citation("RIVER")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RIVER")
Documentation
| HTML | R Script | RIVER |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, BiomedicalInformatics, Clustering, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomicVariation, Regression, SNP, Software, SystemsBiology, Transcription, TranscriptomeVariant, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3.2) |
| Imports | glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, testthat, devtools |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/ipw012/RIVER |
| BugReports | https://github.com/ipw012/RIVER/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RIVER_1.0.0.tar.gz |
| Windows Binary | RIVER_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | RIVER_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RIVER |
| Package Short Url | http://bioconductor.org/packages/RIVER/ |
| Package Downloads Report | Download Stats |
Documentation »
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