Package: ELMER
Title: Inferring Regulatory Element Landscapes and Transcription Factor
        Networks Using Cancer Methylomes
Version: 2.32.0
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
VignetteBuilder: knitr
Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
        methods, parallel, stats, utils, IRanges, GenomeInfoDb,
        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: RELEASE_3_21
git_last_commit: b1c7e3b
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-16
NeedsCompilation: no
Packaged: 2025-04-16 22:57:05 UTC; biocbuild
Author: Tiago Chedraoui Silva [aut, cre],
  Lijing Yao [aut],
  Simon Coetzee [aut],
  Nicole Gull [ctb],
  Hui Shen [ctb],
  Peter Laird [ctb],
  Peggy Farnham [aut],
  Dechen Li [ctb],
  Benjamin Berman [aut]
Built: R 4.5.0; ; 2025-04-17 12:57:18 UTC; windows
