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 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 additional tools to aid in visualization and analysis of the results, including plots displaying and comparing methylation and expression data and RE DNA 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: 1.0.0
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: 7.3.2
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 (>= 4.5)
Imports: graphics, grDevices, stats, utils, tools, S4Vectors,
        GenomicRanges, IRanges, parallel, pastecs, ggplot2, RCircos,
        survival, BSgenome.Hsapiens.UCSC.hg38, seqLogo, Biostrings,
        matlab, TCGAbiolinks, methods, R.utils, MultiAssayExperiment,
        SummarizedExperiment, sesame, sesameData, AnnotationHub,
        ExperimentHub, TENET.ExperimentHub, rtracklayer
Suggests: TENET.AnnotationHub, knitr, rmarkdown, BiocStyle, MotifDb
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TENET
git_branch: RELEASE_3_21
git_last_commit: 89a329b
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:10:08 UTC; biocbuild
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 4.5.0; ; 2025-04-16 04:09:09 UTC; unix
