Package: QSutils
Type: Package
Title: Quasispecies Diversity
Version: 1.31.0
Date: 2024-04-23
Authors@R: c(person("Mercedes", "Guerrero-Murillo", email="mergumu@gmail.com", role=c("cre", "aut"), comment = c(ORCID = "0000-0002-5556-2460")),  person("Josep", "Gregori i Font", role=c ("aut"), comment = c(ORCID = "0000-0002-4253-8015")))
Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
Imports: ape, stats, psych
Encoding: UTF-8
Description: Set of utility functions for viral quasispecies analysis
        with NGS data. Most functions are equally useful for
        metagenomic studies. There are three main types: (1) data
        manipulation and exploration—functions useful for converting
        reads to haplotypes and frequencies, repairing reads,
        intersecting strand haplotypes, and visualizing haplotype
        alignments. (2) diversity indices—functions to compute
        diversity and entropy, in which incidence, abundance, and
        functional indices are considered. (3) data
        simulation—functions useful for generating random viral
        quasispecies data.
License: GPL-2
biocViews: Software, Genetics, DNASeq, GeneticVariability, Sequencing,
        Alignment, SequenceMatching, DataImport
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, ggplot2
NeedsCompilation: no
Packaged: 2026-07-03 15:14:07 UTC; root
RoxygenNote: 6.0.1
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:48:59 UTC
RemoteUrl: https://github.com/bioc/QSutils
RemoteRef: HEAD
RemoteSha: 67c7b6dd1ff0ba61479384ffeb9967c6305ab831
Author: Mercedes Guerrero-Murillo [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-5556-2460>),
  Josep Gregori i Font [aut] (ORCID:
    <https://orcid.org/0000-0002-4253-8015>)
Maintainer: Mercedes Guerrero-Murillo <mergumu@gmail.com>