Package: epiRomics
Type: Package
Title: Epigenomic Analysis Package Built for R (epiRomics)
Version: 1.0.0
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'
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:07:10 UTC
RemoteUrl: https://github.com/bioc/epiRomics
RemoteRef: RELEASE_3_23
RemoteSha: 7332a8dcfe59de4eb29874aa6294387bd18c1b2d
NeedsCompilation: no
Packaged: 2026-04-29 21:10:13 UTC; root
Author: Alex M. Mawla [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0907-464X>),
  Mark O. Huising [aut] (ORCID: <https://orcid.org/0000-0002-6594-2205>)
Maintainer: Alex M. Mawla <ammawla@ucdavis.edu>
Built: R 4.6.0; ; 2026-04-29 22:10:30 UTC; unix
