Package: ProActive
Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Version: 0.1.0.9000
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Authors@R: 
  c(person(given = "Jessie",
           family = "Maier",
           role = c("aut", "cre", "cph"),
           email = "jlmaier@ncsu.edu",
           comment = c(ORCID = "0009-0001-8575-5386")),
    person(given = "Manuel",
           family = "Kleiner",
           role= c("aut", "ths"),
           comment = c(ORCID = "0000-0001-6904-0287")))
Description: Automate the detection of gaps and elevations in mapped
        sequencing read coverage using a 2D pattern-matching algorithm.
        'ProActive' detects, characterizes and visualizes read coverage
        patterns in both genomes and metagenomes. Optionally, users may
        provide gene annotations associated with their genome or
        metagenome in the form of a .gff file. In this case,
        'ProActive' will generate an additional output table containing
        the gene annotations found within the detected regions of
        gapped and elevated read coverage. Additionally, users can
        search for gene annotations of interest in the output read
        coverage plots.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
URL: https://github.com/jlmaier12/ProActive,
        https://jlmaier12.github.io/ProActive/
BugReports: https://github.com/jlmaier12/ProActive/issues
Imports: utils, stats, dplyr, ggplot2, stringr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), kableExtra
VignetteBuilder: knitr
Depends: R (>= 4.2.0)
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev
Repository: https://jlmaier12.r-universe.dev
Date/Publication: 2025-08-08 01:17:23 UTC
RemoteUrl: https://github.com/jlmaier12/proactive
RemoteRef: HEAD
RemoteSha: fe522fb8d5484bab74ce179a743e493596ee281b
NeedsCompilation: no
Packaged: 2026-10-13 13:40:45 UTC; root
Author: Jessie Maier [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0001-8575-5386>),
  Manuel Kleiner [aut, ths] (ORCID:
    <https://orcid.org/0000-0001-6904-0287>)