Package: TENET
Title: R package for TENET (Tracing regulatory Element Networks using
        Epigenetic Traits) to identify key transcription factors
Description: TENET identifies key transcription factors (TFs) and
        regulatory elements (REs) linked to a specific cell type by
        finding significantly correlated differences in gene expression
        and RE DNA methylation between case and control input datasets,
        and identifying the top genes by number of significant RE DNA
        methylation site links. It also includes many tools for
        visualization and analysis of the results, including plots
        displaying and comparing methylation and expression data and
        methylation site link counts, survival analysis, TF motif
        searching in the vicinity of linked RE DNA methylation sites,
        custom TAD and peak overlap analysis, and UCSC Genome Browser
        track file generation. A utility function is also provided to
        download methylation, expression, and patient survival data
        from The Cancer Genome Atlas (TCGA) for use in TENET or other
        analyses.
Version: 1.2.0
Authors@R: c(person("Rhie Lab at the University of Southern California", email = "rhielab@gmail.com", role = "cre"), person("Daniel", "Mullen", role = "aut", comment = c(ORCID = "0000-0002-7639-0549")), person("Zexun", "Wu", role = "aut", comment = c(ORCID = "0000-0003-2566-1326")), person("Ethan", "Nelson-Moore", role = "aut", comment = c(ORCID = "0009-0001-6903-9232")), person("Suhn", "Rhie", role = "aut", comment = c(ORCID = "0000-0002-5522-5296")))
URL: https://github.com/rhielab/TENET
BugReports: https://github.com/rhielab/TENET/issues
License: GPL-2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
BiocType: Software
biocViews: Software, BiomedicalInformatics, CellBiology, Genetics,
        Epigenetics, MultipleComparison, GeneExpression,
        DifferentialExpression, DNAMethylation,
        DifferentialMethylation, MethylationArray, Sequencing,
        MethylSeq, RNASeq, FunctionalGenomics, GeneRegulation,
        GeneTarget, HistoneModification, Transcription,
        Transcriptomics, Survival, Visualization
Depends: R (>= 4.4)
Imports: graphics, grDevices, stats, utils, tools, S4Vectors,
        GenomicRanges, IRanges, parallel, pastecs, ggplot2 (>= 4.0),
        RCircos, survival, BSgenome.Hsapiens.UCSC.hg38, seqLogo,
        Biostrings, matlab, TCGAbiolinks, methods, R.utils,
        MultiAssayExperiment, SummarizedExperiment, sesame, sesameData,
        AnnotationHub, ExperimentHub, TENET.ExperimentHub, rtracklayer,
        MotifDb, BAMMtools, survminer
Suggests: TENET.AnnotationHub, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:34:59 UTC
RemoteUrl: https://github.com/bioc/TENET
RemoteRef: RELEASE_3_22
RemoteSha: b0a4fcf20ac58660d41b453944392e641366f713
NeedsCompilation: no
Packaged: 2025-11-11 18:20:00 UTC; root
Author: Rhie Lab at the University of Southern California [cre],
  Daniel Mullen [aut] (ORCID: <https://orcid.org/0000-0002-7639-0549>),
  Zexun Wu [aut] (ORCID: <https://orcid.org/0000-0003-2566-1326>),
  Ethan Nelson-Moore [aut] (ORCID:
    <https://orcid.org/0009-0001-6903-9232>),
  Suhn Rhie [aut] (ORCID: <https://orcid.org/0000-0002-5522-5296>)
Maintainer: Rhie Lab at the University of Southern California <rhielab@gmail.com>
Built: R 4.5.2; ; 2025-11-11 18:28:08 UTC; windows
