DESCRIPTION

Type: Package
Package: EpiCompare
Title: Comparison, Benchmarking & QC of Epigenomic Datasets
Version: 1.9.10
Authors@R: c(
    person(given = "Sera", family = "Choi", 
        email = "serachoi1230@gmail.com", 
        role = "aut",
        comment = c(ORCID = "0000-0002-5077-1984")),
    person(given="Brian", family="Schilder", 
        email = "brian_schilder@alumni.brown.edu", 
        role = "aut",
        comment = c(ORCID = "0000-0001-5949-2191")),
     person(given="Leyla", family="Abbasova", 
        email = "profernitsky@gmail.com", 
        role = "aut"), 
    person(given="Alan", family="Murphy", 
        email = "alanmurph94@hotmail.com", 
        role = "aut",
        comment = c(ORCID = "0000-0002-2487-8753")),
    person(given="Nathan", family="Skene", 
        email = "nathan.skene@gmail.com", 
        role = "aut",
        comment = c(ORCID = "0000-0002-6807-3180")),
    person(given="Thomas", family="Roberts",
        email = "tomroberts.work15@gmail.com",
        role = "ctb"),
    person(given="Hiranyamaya", family="Dash", 
        email = "hdash.work@gmail.com",
        role = "cre",
        comment = c(ORCID = "0009-0005-5514-505X"))
  )
Description: EpiCompare is used to compare and analyse epigenetic datasets 
  for quality control and benchmarking purposes. 
  The package outputs an HTML report consisting of three sections: 
  (1. General metrics) Metrics on peaks (percentage of blacklisted and 
  non-standard peaks, and peak widths) and fragments (duplication rate) 
  of samples, 
  (2. Peak overlap) Percentage and statistical significance of 
  overlapping and non-overlapping peaks. Also includes upset plot and 
  (3. Functional annotation) functional annotation 
  (ChromHMM, ChIPseeker and enrichment analysis) of peaks. 
  Also includes peak enrichment around TSS.
License: GPL-3
URL: https://github.com/neurogenomics/EpiCompare
BugReports: https://github.com/neurogenomics/EpiCompare/issues
Depends: 
    R (>= 4.2.0)
Imports:
    AnnotationHub,
    ChIPseeker,
    data.table,
    genomation,
    GenomicRanges,
    IRanges,
    GenomeInfoDb,
    ggplot2 (>= 3.5.0),
    htmltools,
    methods,
    plotly, 
    reshape2,
    rmarkdown,
    rtracklayer,
    stats,
    stringr,
    utils,
    BiocGenerics,
    downloadthis,
    parallel
Suggests: 
    rworkflows,
    BiocFileCache,
    BiocParallel,
    BiocStyle,
    clusterProfiler,
    GenomicAlignments,
    grDevices,
    knitr,
    org.Hs.eg.db,
    testthat (>= 3.0.0),
    tidyr,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Mmusculus.UCSC.mm9.knownGene,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Hsapiens.UCSC.hg38,
    BSgenome.Mmusculus.UCSC.mm9,
    BSgenome.Mmusculus.UCSC.mm10,
    ComplexUpset,
    plyranges,
    scales,
    Matrix,
    consensusSeekeR,
    heatmaply,
    viridis
VignetteBuilder: 
    knitr
biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
    MultipleComparison, FunctionalGenomics, ATACSeq, DNaseSeq
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 7.3.2