tidyGenR: Tidy Multilocus Amplicon Genotypes

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.

Version:	0.1.7
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
Published:	2026-02-17
DOI:	10.32614/CRAN.package.tidyGenR
Author:	Miguel Camacho [aut, cre, cph], Jennifer Leonard [fnd]
Maintainer:	Miguel Camacho <miguelcamachosanchez at gmail.com>
BugReports:	https://github.com/csmiguel/tidyGenR/issues
License:	GPL (≥ 3)
URL:	https://github.com/csmiguel/tidyGenR
NeedsCompilation:	no
SystemRequirements:	cutadapt >=2.0 (https://cutadapt.readthedocs.io/en/stable/)
Materials:	NEWS
CRAN checks:	tidyGenR results

Documentation:

Reference manual:	tidyGenR.html , tidyGenR.pdf
Vignettes:	tidyGenR-intro (source, R code) tidyGenR-optimization (source, R code)

Downloads:

Package source:	tidyGenR_0.1.7.tar.gz
Windows binaries:	r-devel: tidyGenR_0.1.7.zip, r-release: tidyGenR_0.1.7.zip, r-oldrel: tidyGenR_0.1.7.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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