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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.
| Version: | 0.1.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | dplyr, googlesheets4, phyloseq, purrr, rlang, tibble, tidyr, vegan, ggplot2, vroom, Biostrings, stringr, tidyselect, readr |
| Suggests: | insect, testthat, tidyverse, knitr, rmarkdown |
| Published: | 2025-10-01 |
| DOI: | 10.32614/CRAN.package.eDNAfuns (may not be active yet) |
| Author: | Ramón Gallego Simón [aut, cre] |
| Maintainer: | Ramón Gallego Simón <ramongallego at gmail.com> |
| License: | GPL (≥ 3) |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | eDNAfuns results |
| Reference manual: | eDNAfuns.html , eDNAfuns.pdf |
| Package source: | eDNAfuns_0.1.0.tar.gz |
| Windows binaries: | r-devel: eDNAfuns_0.1.0.zip, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): eDNAfuns_0.1.0.tgz, r-oldrel (x86_64): eDNAfuns_0.1.0.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.