Package: QSutils
Type: Package
Title: Quasispecies Diversity
Version: 1.26.0
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: 2025-04-16 03:02:35 UTC; biocbuild
RoxygenNote: 6.0.1
git_url: https://git.bioconductor.org/packages/QSutils
git_branch: RELEASE_3_21
git_last_commit: b766e3c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
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>
Built: R 4.5.0; ; 2025-04-16 15:13:51 UTC; windows
