Package: ELMER
Title: Inferring Regulatory Element Landscapes and Transcription Factor
        Networks Using Cancer Methylomes
Version: 2.35.1
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, 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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev perl libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-02-04 06:30:54 UTC
RemoteUrl: https://github.com/bioc/ELMER
RemoteRef: HEAD
RemoteSha: ecf8042100dc22fb6b9f620b1835a96cdc758e51
NeedsCompilation: no
Packaged: 2026-02-05 04:24:03 UTC; root
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 4.6.0; ; 2026-02-05 04:27:32 UTC; windows
