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

 

   

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
PDF   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) (< 6 months)
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.

Package Source 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
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RIVER/tree/release-3.5
Package Short Url http://bioconductor.org/packages/RIVER/
Package Downloads Report Download Stats

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