Package: eDNAfuns
Type: Package
Title: Working with Metabarcoding Data in a Tidy Format
Version: 0.1.0
Authors@R: person(given = "Ramón",
                family= c("Gallego Simón"),
                role= c("aut","cre"),
                email= "ramongallego@gmail.com")
Description: A series of R functions that come in handy while working with metabarcoding data.
  The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way.
  In a way it is all about putting together the grammar of the  'tidyverse' from Wickham et al.(2019) <doi:10.21105/joss.01686> 
  with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x>
  and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>.
  The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'),
  to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package
  works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: insect, testthat, tidyverse, knitr, rmarkdown
Imports: dplyr, googlesheets4, phyloseq, purrr, rlang, tibble, tidyr,
        vegan, ggplot2, vroom, Biostrings, stringr, tidyselect, readr
Depends: R (>= 4.1.0)
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-09-24 10:08:22 UTC; RG.5015511
Author: Ramón Gallego Simón [aut, cre]
Maintainer: Ramón Gallego Simón <ramongallego@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-01 07:00:09 UTC
Built: R 4.6.0; ; 2026-04-29 16:15:04 UTC; unix
