Package: rhinotypeR
Type: Package
Title: Rhinovirus genotyping
Version: 1.7.3
Date: 2026-07-03
Authors@R: c(
    person("Martha", "Luka", role = c("aut", "cre"), email = "marthaluka20@gmail.com",
           comment = c(ORCID = "0000-0001-6217-4426")),
    person("Ruth", "Nanjala", role = c("aut")),
    person("Winfred", "Gatua", role = c("aut")),
    person("Wafaa M.", "Rashed", role = c("aut")),
    person("Olaitan", "Awe", role = c("aut"))
    )
Description: "rhinotypeR" is designed to automate the comparison of
        sequence data against prototype strains, streamlining the
        genotype assignment process. By implementing predefined
        pairwise distance thresholds, this package makes genotype
        assignment accessible to researchers and public health
        professionals. This tool enhances our epidemiological toolkit
        by enabling more efficient surveillance and analysis of
        rhinoviruses (RVs) and other viral pathogens with complex
        genomic landscapes. Additionally, "rhinotypeR" supports
        comprehensive visualization and analysis of single nucleotide
        polymorphisms (SNPs) and amino acid substitutions, facilitating
        in-depth genetic and evolutionary studies.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Biostrings, methods, MSA2dist, msa
LazyData: false
biocViews: Sequencing, Genetics, Phylogenetics, Visualization,
        MultipleSequenceAlignment, MultipleComparison
Depends: R (>= 4.5.0), MultipleAlignment
Suggests: knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
VignetteBuilder: knitr
Vignettes: `Introduction to rhinotypeR` = "vignettes/rhinotypeR.Rmd"
URL: https://github.com/omicscodeathon/rhinotypeR
BugReports: https://github.com/omicscodeathon/rhinotypeR/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-03 14:14:55 UTC
RemoteUrl: https://github.com/bioc/rhinotypeR
RemoteRef: HEAD
RemoteSha: 94000ac0b014baa1e1acbcf4dcff5025e08ecd03
NeedsCompilation: no
Packaged: 2026-07-03 15:10:01 UTC; root
Author: Martha Luka [aut, cre] (ORCID: <https://orcid.org/0000-0001-6217-4426>),
  Ruth Nanjala [aut],
  Winfred Gatua [aut],
  Wafaa M. Rashed [aut],
  Olaitan Awe [aut]
Maintainer: Martha Luka <marthaluka20@gmail.com>