DESCRIPTION

Package: RIVER
Title: R package for RIVER (RNA-Informed Variant Effect on Regulation)
Description: 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.
Version: 0.99.9
Authors@R: c(person("Yungil", "Kim", role = c("aut", "cre"), email = "ipw012@gmail.com"),
        person("Damani", "Farhan", role = "ctb", email = "farhand7@gmail.com"),
        person("Alexis", "Battle", role = "aut", email = "ajbattle@cs.jhu.edu"))
Author: Yungil Kim [aut, cre], Alexis Battle [aut]
Maintainer: Yungil Kim <ipw012@gmail.com>
URL: https://github.com/ipw012/RIVER
BugReports: https://github.com/ipw012/RIVER/issues
Depends: R (>= 3.4)
biocViews: GeneExpression, GeneticVariability, SNP, Transcription, FunctionalPrediction, 
        GeneRegulation, GenomicVariation, BiomedicalInformatics, FunctionalGenomics, 
        Genetics, SystemsBiology, Transcriptomics, Bayesian, Clustering, 
        TranscriptomeVariant, Regression
Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils
License: GPL (>= 2)
RoxygenNote: 6.0.1
LazyData: true
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools