Package: cogeqc
Title: Systematic quality checks on comparative genomics analyses
Version: 1.16.0
Date: 2022-01-26
Authors@R: 
    c(
    person(given = "Fabrício",
           family = "Almeida-Silva",
           role = c("aut", "cre"),
           email = "fabricio_almeidasilva@hotmail.com",
           comment = c(ORCID = "0000-0002-5314-2964")),
    person(given = "Yves",
           family = "Van de Peer",
           role = "aut",
           email = "yves.vandepeer@psb.vib-ugent.be",
           comment = c(ORCID = "0000-0003-4327-3730"))
    )
Description: cogeqc aims to facilitate systematic quality checks on
        standard comparative genomics analyses to help researchers
        detect issues and select the most suitable parameters for each
        data set. cogeqc can be used to asses: i. genome assembly and
        annotation quality with BUSCOs and comparisons of statistics
        with publicly available genomes on the NCBI; ii. orthogroup
        inference using a protein domain-based approach and; iii.
        synteny detection using synteny network properties. There are
        also data visualization functions to explore QC summary
        statistics.
License: GPL-3
URL: https://github.com/almeidasilvaf/cogeqc
BugReports: https://support.bioconductor.org/t/cogeqc
biocViews: Software, GenomeAssembly, ComparativeGenomics,
        FunctionalGenomics, Phylogenetics, QualityControl, Network
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
SystemRequirements: BUSCO (>= 5.1.3) <https://busco.ezlab.org/>
Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales,
        ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite,
        Biostrings
Depends: R (>= 4.2.0)
Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
        rmarkdown, covr
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:58:19 UTC
RemoteUrl: https://github.com/bioc/cogeqc
RemoteRef: RELEASE_3_23
RemoteSha: 3b0293af6a357548fd66b422c35f6a2f085c3d8f
NeedsCompilation: no
Packaged: 2026-04-29 20:42:36 UTC; root
Author: Fabrício Almeida-Silva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5314-2964>),
  Yves Van de Peer [aut] (ORCID: <https://orcid.org/0000-0003-4327-3730>)
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>
Built: R 4.6.0; ; 2026-04-29 20:45:53 UTC; windows
