epiRomics/DESCRIPTION at main · Huising-Lab/epiRomics · GitHub

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Package: epiRomics
Type: Package
Title: Epigenomic Analysis Package Built for R (epiRomics)
Version: 0.99.5
Authors@R:
    c(person(given = "Alex M.",
             family = "Mawla",
             role = c("aut", "cre"),
             email = "ammawla@ucdavis.edu",
             comment = c(ORCID = "0000-0003-0907-464X")),
      person(given = "Mark O.",
             family = "Huising",
             role = "aut",
             email = "mhuising@ucdavis.edu",
             comment = c(ORCID = "0000-0002-6594-2205")))
Description: Integrates various levels of epigenomic information, including
    ChIP-seq, histone modification, ATAC-seq, and RNA-seq data. Regulatory
    network analysis uses combinatory approaches to infer regions of
    significance, such as enhancers. Downstream analysis identifies
    co-occurrence of epigenomic data at regions of interest. Visualization
    functions display multi-track genomic views with signal overlays.
    Please contact <ammawla@ucdavis.edu> for suggestions, feedback, or bug
    reporting.
License: Artistic-2.0
Depends:
    R (>= 4.5.0)
URL: https://huising-lab.github.io/epiRomics/, https://github.com/Huising-Lab/epiRomics
BugReports: https://github.com/Huising-Lab/epiRomics/issues
biocViews: Epigenetics, ChIPSeq, ATACSeq, RNASeq, Visualization, Sequencing,
    Software, HistoneModification, GeneRegulation, Transcription,
    FunctionalGenomics
Imports:
    AnnotationDbi (>= 1.68.0),
    annotatr (>= 1.32.0),
    BiocGenerics (>= 0.52.0),
    ChIPseeker (>= 1.42.0),
    data.table (>= 1.15.0),
    digest (>= 0.6.35),
    GenomeInfoDb (>= 1.42.0),
    GenomicFeatures (>= 1.58.0),
    GenomicRanges (>= 1.58.0),
    graphics,
    grDevices,
    IRanges (>= 2.40.0),
    methods,
    rtracklayer (>= 1.66.0),
    S4Vectors (>= 0.44.0),
    stats,
    tools,
    utils
Suggests:
    BiocFileCache (>= 2.14.0),
    knitr,
    org.Hs.eg.db (>= 3.20.0),
    org.Mm.eg.db (>= 3.20.0),
    parallel,
    rmarkdown,
    testthat (>= 3.0.0),
    TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.18.0),
    TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.10.0)
Config/testthat/edition: 3
ByteCompile: true
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Collate:
    'class-epiRomics.R'
    'accessors.R'
    'benchmark_enhancer_predictor.R'
    'build_database.R'
    'cache.R'
    'chromatin_states.R'
    'enhanceosomes.R'
    'enhancers.R'
    'epiRomics-package.R'
    'filter_enhancers.R'
    'plot_quick_view.R'
    'plot_tracks_fast.R'
    'predictors.R'
    'putative_enhancers.R'
    'regions_of_interest.R'
    'synthetic-data.R'
    'tf_overlap.R'
    'utils.R'
    'visualizations.R'
    'zzz-deprecated.R'
    'zzz.R'