Package: longreadvqs
Title: Viral Quasispecies Comparison from Long-Read Sequencing Data
Version: 0.1.5
Authors@R: person("Nakarin", "Pamornchainavakul", email = "pamornakarin@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0378-0316"))
Description: Performs variety of viral quasispecies diversity analyses
        [see Pamornchainavakul et al. (2026)
        <doi:10.1371/journal.pcbi.1014208>] based on long-read sequence
        alignment. Main functions include 1) sequencing error and other
        noise minimization and read sampling, 2) Single nucleotide
        variant (SNV) profiles comparison, and 3) viral quasispecies
        profiles comparison and visualization.
License: GPL-3
URL: https://github.com/NakarinP/longreadvqs
BugReports: https://github.com/NakarinP/longreadvqs/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews:
Imports: ape, Biostrings, cowplot, dplyr, ggplot2, ggpubr, grDevices,
        IRanges, magrittr, methods, plyr, purrr, pwalign, QSutils,
        RColorBrewer, reshape2, scales, seqinr, stats, stringdist,
        stringr, tibble, tidyr
Depends: R (>= 4.4)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev zlib1g-dev
Repository: https://nakarinp.r-universe.dev
Date/Publication: 2026-04-28 22:57:58 UTC
RemoteUrl: https://github.com/nakarinp/longreadvqs
RemoteRef: HEAD
RemoteSha: bb24b5dfc302d03bbfb34b136e96622d3aa5154d
NeedsCompilation: no
Packaged: 2026-10-19 08:11:23 UTC; root
Author: Nakarin Pamornchainavakul [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0378-0316>)
Maintainer: Nakarin Pamornchainavakul <pamornakarin@gmail.com>