DESCRIPTION

Package: HorGeneVis
Type: Package
Title: Horizontal Gene Transfer Visualization
Version: 1.0.0
Authors@R: c(
    person("Jana", "Schwarzerova", email = "Jana.Schwarzerova@vut.cz", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-2918-9313")),
    person("Laxmipriya", "Rajasekaran", role = "aut", comment = c(ORCID = "0009-0000-6401-7731")),
    person("Katerina", "Jureckova", role = "aut", comment = c(ORCID = "0000-0001-5143-9521")),
    person("Julie", "Nejezchlebova", role = "aut", comment = c(ORCID = "0009-0008-2290-6467")),
    person("Margaret", "Varga", role = "aut", comment = c(ORCID = "0000-0002-9086-1626")),
    person("Valentine", "Provaznik", role = "aut", comment = c(ORCID = "0000-0002-3422-7938")),
    person("Wolfram", "Weckwerth", role = "aut", comment = c(ORCID = "0000-0002-9719-6358")),
    person("Darina", "Cejkova", role = c("aut", "fnd"), comment = c(ORCID = "0000-0002-6989-6330"))
    )
Description:
    This package involves the analysis and visualization of horizontal gene transfer (HGT) between individual taxonomic
    categories using genomic data. The tool combines the integration of a heat-map matrix with phylogenetic analysis
    visualization techniques to enhance the accuracy and efficiency of HGT event detection. We applied it to a diverse
    set of bacterial genomes from chicken and pig gut and expanded the results with established methods for HGT
    detection. The findings demonstrate the capability of our visualization techniques to pinpoint HGT events, offering
    a valuable tool for researchers to explore the intricate dynamics of bacterial genome evolution.
License: GPL-3
Encoding: UTF-8
Imports: 
    ape,
    circlize,
    RColorBrewer
References:
    - Schwarzerova, J., Rajasekaran, L., Jureckova, K., Nejezchlebova, J., Varga, M., Provaznik, V., et al. (2024).
      “Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria,” in Bioinformatics and
      Biomedical Engineering, 1–11.
    - Schwarzerova, J., Zeman, M., Babak, V., Jureckova, K., Nykrynova, M., Varga, M., et al. (2024).
      Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within
      the mobilome through advanced comparative analysis. Microbiol. Spectr. 12, e01964-23. doi:10.1128/spectrum.01964-23.
URL: https://github.com/JanaSchwarzerova/HorGeneVis
BugReports: https://github.com/JanaSchwarzerova/HorGeneVis/issues
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)