Package: ELViS
Title: An R Package for Estimating Copy Number Levels of Viral Genome
        Segments Using Base-Resolution Read Depth Profile
Version: 1.2.0
Authors@R: c(
    person("Hyo Young", "Choi", , "hyoyoung.choi@uthsc.edu", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0002-7627-8493")),
    person("Jin-Young", "Lee", , "jlee307@uthsc.edu", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-5366-7488")),
    person("Xiaobei", "Zhao", , "xiaobei_zhao@uthsc.edu", role = "ctb",
           comment = c(ORCID = "0000-0002-5277-0846")),
    person("Jeremiah R.", "Holt", , "jholt41@uthsc.edu", role = "ctb",
           comment = c(ORCID = "0000-0002-5201-5015")),
    person("Katherine A.", "Hoadley", , "hoadley@med.unc.edu", role = "aut",
           comment = c(ORCID = "0000-0002-1216-477X")),
    person("D. Neil", "Hayes", , "Neil.Hayes@uthsc.edu", role = c("aut", "fnd", "cph"),
           comment = c(ORCID = "0000-0001-6203-7771"))
  )
Description: Base-resolution copy number analysis of viral genome.
        Utilizes base-resolution read depth data over viral genome to
        find copy number segments with two-dimensional segmentation
        approach. Provides publish-ready figures, including histograms
        of read depths, coverage line plots over viral genome annotated
        with copy number change events and viral genes, and heatmaps
        showing multiple types of data with integrative clustering of
        samples.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: CopyNumberVariation, Coverage, GenomicVariation,
        BiomedicalInformatics, Sequencing, Normalization,
        Visualization, Clustering
LazyData: false
BugReports: https://github.com/hyochoi/ELViS/issues
URL: https://github.com/hyochoi/ELViS
Config/testthat/edition: 3
Imports: reticulate, BiocGenerics, circlize, ComplexHeatmap,
        data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2,
        glue, graphics, grDevices, igraph, IRanges, magrittr, memoise,
        methods, parallel, patchwork, scales, segclust2d, stats,
        stringr, txdbmaker, utils, uuid, zoo
Depends: R (>= 4.4.0)
Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0)
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev perl python3 xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:34:26 UTC
RemoteUrl: https://github.com/bioc/ELViS
RemoteRef: RELEASE_3_22
RemoteSha: c2a03f64e4fcfafed26e38aa444c5b17b91d63ac
NeedsCompilation: no
Packaged: 2026-02-18 08:06:18 UTC; root
Author: Hyo Young Choi [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-7627-8493>),
  Jin-Young Lee [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-5366-7488>),
  Xiaobei Zhao [ctb] (ORCID: <https://orcid.org/0000-0002-5277-0846>),
  Jeremiah R. Holt [ctb] (ORCID: <https://orcid.org/0000-0002-5201-5015>),
  Katherine A. Hoadley [aut] (ORCID:
    <https://orcid.org/0000-0002-1216-477X>),
  D. Neil Hayes [aut, fnd, cph] (ORCID:
    <https://orcid.org/0000-0001-6203-7771>)
Maintainer: Jin-Young Lee <jlee307@uthsc.edu>
Built: R 4.5.2; ; 2026-02-18 08:08:35 UTC; windows
