Package: ELViS
Title: An R Package for Estimating Copy Number Levels of Viral Genome
        Segments Using Base-Resolution Read Depth Profile
Version: 1.0.0
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: basilisk, 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 (>= 4.5.0)
Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0)
git_url: https://git.bioconductor.org/packages/ELViS
git_branch: RELEASE_3_21
git_last_commit: 05a3c20
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:25:37 UTC; biocbuild
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 4.5.0; ; 2025-04-16 14:23:40 UTC; windows
