Package: demulticoder
Title: Simultaneous Analysis of Multiplexed Metabarcodes
Version: 0.1.2
Authors@R: c(person("Martha A.", "Sudermann", email = "sudermam@oregonstate.edu", role = c("aut", "cre", "cph")), person("Zachary S. L", "Foster", role = "aut"), person("Samantha", "Dawson", role = "aut"), person("Hung", "Phan", role = "aut"), person("Jeff", "H. Chang", role = "aut"), person("Niklaus", "Grünwald", role = c("aut", "cph"))) 
Description: A comprehensive set of wrapper functions for the analysis of multiplex metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2' to trim primers, filter reads, perform amplicon sequence variant (ASV) inference, and assign taxonomy. The package can handle single metabarcode datasets, datasets with two pooled metabarcodes, or multiple datasets simultaneously. The final output is a matrix per metabarcode, containing both ASV abundance data and associated taxonomic assignments. An optional function converts these matrices into 'phyloseq' and 'taxmap' objects. For more information on 'DADA2', including information on how DADA2 infers samples sequences, see Callahan et al. (2016) <doi:10.1038/nmeth.3869>. For more details on the demulticoder R package see Sudermann et al. (2025) <doi:10.1094/PHYTO-02-25-0043-FI>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.0.2)
Imports: furrr, purrr, readr, stringr, tidyr, dplyr, ggplot2, tibble,
        utils
Suggests: BiocManager, Biostrings, dada2, metacoder, ShortRead,
        phyloseq, rmarkdown, RcppParallel, testthat (>= 3.0.0)
Config/testthat/edition: 3
URL: https://grunwaldlab.github.io/demulticoder/,
        https://github.com/grunwaldlab/demulticoder
BugReports: https://github.com/grunwaldlab/demulticoder/issues
RoxygenNote: 7.3.2
Config/Needs/website: rmarkdown
NeedsCompilation: no
Packaged: 2025-04-30 21:59:31 UTC; marthasudermann
Maintainer: Martha A. Sudermann <sudermam@oregonstate.edu>
Author: Martha A. Sudermann [aut, cre, cph],
  Zachary S. L Foster [aut],
  Samantha Dawson [aut],
  Hung Phan [aut],
  Jeff H. Chang [aut],
  Niklaus Grünwald [aut, cph]
Repository: CRAN
Date/Publication: 2025-05-05 09:50:02 UTC
Built: R 4.4.3; ; 2025-12-22 04:45:52 UTC; windows
