Package: tidyGenR
Title: Tidy Multilocus Amplicon Genotypes
Version: 0.1.8
Authors@R: c(
    person("Miguel", "Camacho", , "miguelcamachosanchez@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-6385-7963")),
    person("Jennifer", "Leonard", role = "fnd")
  )
Description: Variant determination and genotyping from high throughput
        sequences from multilocus amplicon libraries, typically
        sequenced in Illumina MiSeq or similar. It provides a set of
        core functions for the central steps: demultiplex by locus,
        truncate reads, variant calling, and genotype calling.
        Additionally, it provides a set of functions for diagnosis and
        estimation of best running parameters and multiple extensions
        for genotype/variants manipulation and reformatting. Output
        variants and genotypes are output in 'tidy' format, thus
        facilitating reformatting, manipulation and potential
        connection to other R packages.
License: GPL (>= 3)
URL: https://github.com/csmiguel/tidyGenR
BugReports: https://github.com/csmiguel/tidyGenR/issues
Depends: R (>= 4.1.0)
Imports: Biostrings, dada2 (>= 1.16), digest, dplyr (>= 1.0.0),
        ggplot2, glue, methods, plyr, readr, ShortRead (>= 1.32.0),
        stats, stringr, tibble, tidyr (>= 1.1.0), tidyselect, DECIPHER,
        patchwork, writexl
Suggests: ape, knitr, rmarkdown, testthat (>= 3.0.0), tools, BiocStyle
biocViews: Software, Sequencing, Classification, Phylogenetics
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
Packaged: 2026-07-14 05:58:22 UTC; root
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
SystemRequirements: cutadapt >=2.0
        (https://cutadapt.readthedocs.io/en/stable/)
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libx11-dev xz-utils zlib1g-dev
Repository: https://csmiguel.r-universe.dev
Date/Publication: 2026-05-15 10:59:16 UTC
RemoteUrl: https://github.com/csmiguel/tidygenr
RemoteRef: HEAD
RemoteSha: c8f9e1eae7b105dd30fb2987897a2b25f2994180
Author: Miguel Camacho [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6385-7963>),
  Jennifer Leonard [fnd]
Maintainer: Miguel Camacho <miguelcamachosanchez@gmail.com>