DESCRIPTION

Type: Package
Package: MotifPeeker
Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Version: 0.99.13
Authors@R: c( 
    person(given = "Hiranyamaya",
           family = "Dash",
           role = c("cre", "aut"),
           email = "hdash.work@gmail.com",
           comment = c(ORCID = "0009-0005-5514-505X")),
    person(given = "Thomas",
           family = "Roberts",
           role = c("aut"),
           email = "tomroberts.work15@gmail.com",
           comment = c(ORCID = "0009-0006-6244-8670")),
    person(given = "Maria",
           family = "Weinert",
           role = c("aut"),
           email = "m.weinert13@imperial.ac.uk",
           comment = c(ORCID = "0000-0001-6187-1000")),     
    person(given = "Nathan",
           family = "Skene",
           role = c("aut"),
           email = "nathan.skene@gmail.com",
           comment = c(ORCID = "0000-0002-6807-3180"))
    )
Description: MotifPeeker is used to compare and analyse datasets from
    epigenomic profiling methods with motif enrichment as the key
    benchmark.  The package outputs an HTML report consisting of three
    sections: (1. General Metrics) Overview of peaks-related general
    metrics for the datasets (FRiP scores, peak widths and motif-summit
    distances).  (2. Known Motif Enrichment Analysis) Statistics for the
    frequency of user-provided motifs enriched in the datasets.  (3.
    De-Novo Motif Enrichment Analysis) Statistics for the frequency of
    de-novo discovered motifs enriched in the datasets and compared with
    known motifs.
License: GPL (>= 3)
URL: https://github.com/neurogenomics/MotifPeeker
BugReports: https://github.com/neurogenomics/MotifPeeker/issues
Depends: 
    R (>= 4.4.0)
Imports:
    BiocFileCache,
    BiocParallel,
    DT,
    ggplot2,
    plotly,
    universalmotif,
    GenomicRanges,
    IRanges,
    rtracklayer,
    tools,
    htmltools,
    rmarkdown,
    viridis,
    SummarizedExperiment,
    htmlwidgets,
    Rsamtools,
    GenomicAlignments,
    GenomeInfoDb,
    Biostrings,
    BSgenome,
    memes,
    S4Vectors,
    dplyr,
    purrr,
    tidyr,
    heatmaply,
    stats,
    utils
Suggests:
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Hsapiens.UCSC.hg38,
    downloadthis,
    knitr,
    markdown,
    methods,
    remotes,
    rworkflows,
    testthat (>= 3.0.0),
    withr,
    emoji,
    curl,
    jsonlite
VignetteBuilder: 
    knitr
biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
    MultipleComparison, FunctionalGenomics, MotifDiscovery,
    SequenceMatching, Software, Alignment
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 7.3.2
SystemRequirements: MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html>