Package: iNETgrate
Type: Package
Title: Integrates DNA methylation data with gene expression in a single
        gene network
Version: 1.11.0
Date: 2023-03-24
Authors@R: c(
    person("Ghazal", "Ebrahimi", role = "aut"),
    person("Isha", "Mehta", role = "aut",
    comment = c(ORCID = "0000-0002-6009-0787")),
    person("Hanie", "Samimi", role = "aut"),
    person("Habil", "Zare", email = "zare@u.washington.edu",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5902-6238")))
biocViews: GeneExpression, RNASeq, DNAMethylation, NetworkInference,
        Network, GraphAndNetwork, BiomedicalInformatics,
        SystemsBiology, Transcriptomics, Classification, Clustering,
        DimensionReduction, PrincipalComponent, mRNAMicroarray,
        Normalization, GenePrediction, KEGG, Survival
Depends: R (>= 4.3.0), BiocStyle (>= 2.18.1)
Description: The iNETgrate package provides functions to build a
        correlation network in which nodes are genes. DNA methylation
        and gene expression data are integrated to define the
        connections between genes. This network is used to identify
        modules (clusters) of genes. The biological information in each
        of the resulting modules is represented by an eigengene. These
        biological signatures can be used as features e.g., for
        classification of patients into risk categories. The resulting
        biological signatures are very robust and give a holistic view
        of the underlying molecular changes.
Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA,
        grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26),
        Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast,
        tidyr, tidyselect, utils
Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db,
        IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi,
        sesameData, TCGAbiolinks (>= 2.29.4)
License: GPL-3
BugReports: https://github.com/Bioconductor/BiocManager/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-07-16 09:32:56 UTC; root
Author: Isha Mehta [aut] (<https://orcid.org/0000-0002-6009-0787>),
        Ghazal Ebrahimi [aut], Hanie Samimi [aut], Habil Zare [aut,
        cre] (<https://orcid.org/0000-0001-5902-6238>)
Maintainer: Habil Zare <zare@u.washington.edu>
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:01:02 UTC
RemoteUrl: https://github.com/bioc/iNETgrate
RemoteRef: HEAD
RemoteSha: 23a996a20753a3e4d40659b93a0eecb1322acfe4