Package: ELMER
Title:
    Inferring Regulatory Element Landscapes and Transcription Factor
    Networks Using Cancer Methylomes
Version: 2.35.0
Authors@R: c( person("Tiago","Chedraoui Silva", role = c("aut","cre"), email = "tiagochst@gmail.com"),
           person("Lijing", "Yao", role = "aut", email = "lijingya@usc.edu"),
		       person("Simon","Coetzee", role = c("aut"), email = "Simon.Coetzee@cshs.org"),
		       person("Nicole", "Gull", role = "ctb"),
		       person("Hui", "Shen", role = "ctb"),
		       person("Peter", "Laird", role = "ctb"),
		       person("Peggy", "Farnham", role = "aut"),
		       person("Dechen", "Li", role = "ctb"),
		       person("Benjamin", "Berman", role = "aut")
		       )
Maintainer:
 Tiago Chedraoui Silva <tiagochst@gmail.com>
Description: ELMER is designed to use DNA methylation and gene expression from a
    large number of samples to infere regulatory element landscape and transcription
    factor network in primary tissue.
Depends:
    R (>= 3.4.0),
    ELMER.data (>= 2.9.3)
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Imports:
    GenomicRanges,
    ggplot2,
    reshape,
    grid, 
    grDevices, 
    graphics, 
    methods,
    parallel, 
    stats, 
    utils,
    IRanges,
    Seqinfo,
    S4Vectors,
    GenomicFeatures,
    TCGAbiolinks (>= 2.23.7),
    plyr,
    Matrix,
    dplyr,
    Gviz, 
    ComplexHeatmap,
    circlize,
    MultiAssayExperiment, 
    SummarizedExperiment,
    biomaRt, 
    doParallel,
    downloader, 
    ggrepel,
    lattice, 
    magrittr, 
    readr, 
    scales,
    rvest,
    xml2,
    plotly,
    gridExtra,
    rmarkdown,
    stringr,
    tibble,
    tidyr,
    progress,
    purrr,
    reshape2,
    ggpubr,
    rtracklayer (>= 1.61.2),
    DelayedArray
Suggests:
    BiocStyle,
    AnnotationHub,
    ExperimentHub,
    knitr,
    testthat,
    data.table, 
    DT,
    GenomicInteractions,
    webshot,
    R.utils,
    covr,
    sesameData
biocViews:
    DNAMethylation, 
    GeneExpression, 
    MotifAnnotation, 
    Software,
    GeneRegulation,
    Transcription, 
    Network
Encoding: UTF-8
RoxygenNote: 7.2.3
git_url: https://git.bioconductor.org/packages/ELMER
git_branch: devel
git_last_commit: 642227c
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
