Package: tidyGenR
Title: Tidy Multilocus Amplicon Genotypes
Version: 0.1.7
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: 2026-02-13 11:33:59 UTC; Miguel
RoxygenNote: 7.3.3
SystemRequirements: cutadapt >=2.0
        (https://cutadapt.readthedocs.io/en/stable/)
Config/testthat/edition: 3
VignetteBuilder: knitr
Author: Miguel Camacho [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6385-7963>),
  Jennifer Leonard [fnd]
Maintainer: Miguel Camacho <miguelcamachosanchez@gmail.com>
Repository: CRAN
Date/Publication: 2026-02-17 22:10:02 UTC
Built: R 4.7.0; ; 2026-05-10 03:46:24 UTC; windows
