Type: Package
Package: MotifPeeker
Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Version: 1.2.0
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, Seqinfo, 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>
git_url: https://git.bioconductor.org/packages/MotifPeeker
git_branch: RELEASE_3_22
git_last_commit: aee3e06
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 04:37:15 UTC; biocbuild
Author: Hiranyamaya Dash [cre, aut] (ORCID:
    <https://orcid.org/0009-0005-5514-505X>),
  Thomas Roberts [aut] (ORCID: <https://orcid.org/0009-0006-6244-8670>),
  Maria Weinert [aut] (ORCID: <https://orcid.org/0000-0001-6187-1000>),
  Nathan Skene [aut] (ORCID: <https://orcid.org/0000-0002-6807-3180>)
Maintainer: Hiranyamaya Dash <hdash.work@gmail.com>
Built: R 4.5.1; ; 2025-10-30 12:26:36 UTC; unix
