RIVER

DOI: 10.18129/B9.bioc.RIVER    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RIVER.

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RIVER")

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("RIVER")

 

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	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RIVER_1.8.0.tar.gz
Windows Binary	RIVER_1.8.0.zip
Mac OS X 10.11 (El Capitan)	RIVER_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RIVER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RIVER
Package Short Url	https://bioconductor.org/packages/RIVER/
Package Downloads Report	Download Stats