Package: iNETgrate
Type: Package
Title: Integrates DNA methylation data with gene expression in a single
        gene network
Version: 1.6.0
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: 2025-04-16 01:30:13 UTC; biocbuild
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>
git_url: https://git.bioconductor.org/packages/iNETgrate
git_branch: RELEASE_3_21
git_last_commit: 299831c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
Built: R 4.5.0; ; 2025-04-16 14:41:56 UTC; windows
