Package: ProActive
Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Version: 0.1.0
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
NeedsCompilation: no
Packaged: 2025-01-20 20:39:54 UTC; jlmaier
Author: Jessie Maier [aut, cre, cph] (<https://orcid.org/0009-0001-8575-5386>),
  Manuel Kleiner [aut, ths] (<https://orcid.org/0000-0001-6904-0287>)
Repository: CRAN
Date/Publication: 2025-01-21 08:00:02 UTC
Built: R 4.7.0; ; 2026-07-17 04:13:46 UTC; windows
