Package: IntOMICS
Type: Package
Title: Integrative analysis of multi-omics data to infer regulatory
        networks
Version: 1.1.0
Authors@R: person("Pacinkova", "Anna", email = "ana.pacinkova@gmail.com", 
    role = c("cre","aut"))
URL: https://github.com/anna-pacinkova/IntOMICS
BugReports: https://github.com/anna-pacinkova/IntOMICS/issues
Description: IntOMICS is an efficient integrative framework based on Bayesian 
    networks. IntOMICS systematically analyses gene expression (GE), 
    DNA methylation (METH), copy number variation (CNV) and biological prior 
    knowledge (B) to infer regulatory networks. IntOMICS complements 
    the missing biological prior knowledge by so-called empirical biological 
    knowledge (empB), estimated from the available experimental data. 
    An automatically tuned MCMC algorithm (Yang and Rosenthal, 2017) estimates 
    model parameters and the empirical biological knowledge. Conventional MCMC 
    algorithm with additional Markov blanket resampling (MBR) step (Su and 
    Borsuk, 2016) infers resulting regulatory network structure consisting 
    of three types of nodes: GE nodes refer to gene expression levels, 
    CNV nodes refer to associated copy number variations, and METH nodes 
    refer to associated DNA methylation probe(s).
Imports: bnlearn, bnstruct, matrixStats, RColorBrewer, bestNormalize,
        igraph, gplots, stats, utils, graphics, numbers,
        SummarizedExperiment, ggplot2, ggraph, methods, cowplot, grid,
        rlang
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
RoxygenNote: 7.2.2
LazyData: false
Suggests: BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils,
        testthat
biocViews: Software, DNAMethylation, GeneExpression,
        CopyNumberVariation, SystemsBiology, GeneRegulation, Network,
        Bayesian
git_url: https://git.bioconductor.org/packages/IntOMICS
git_branch: devel
git_last_commit: 9c86a35
git_last_commit_date: 2023-04-25
Date/Publication: 2023-05-04
NeedsCompilation: no
Packaged: 2023-05-05 00:52:39 UTC; biocbuild
Author: Pacinkova Anna [cre, aut]
Maintainer: Pacinkova Anna <ana.pacinkova@gmail.com>
Built: R 4.3.0; ; 2023-05-05 13:48:53 UTC; windows
