Package: cogeqc
Title: Systematic quality checks on comparative genomics analyses
Version: 1.15.0
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: 7.2.3
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
git_url: https://git.bioconductor.org/packages/cogeqc
git_branch: devel
git_last_commit: 0e2fb28
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-11-12
NeedsCompilation: no
Packaged: 2025-11-12 21:02:11 UTC; biocbuild
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; ; 2025-11-13 01:54:39 UTC; unix
