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: 1.34.0
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 (>= 3.3.2)
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
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:37:54 UTC
RemoteUrl: https://github.com/bioc/RIVER
RemoteRef: RELEASE_3_22
RemoteSha: 88ba126f2f1537f46f8c6609d4f7b9ed6fb0317d
NeedsCompilation: no
Packaged: 2026-02-03 08:30:37 UTC; root
Built: R 4.5.2; ; 2026-02-03 08:32:10 UTC; windows
