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)
Roxygen: list(markdown = TRUE)
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: 2026-06-18 11:11:11 UTC; root
Maintainer: Martha A. Sudermann <sudermam@oregonstate.edu>
Config/pak/sysreqs: libicu-dev libx11-dev
Repository: https://grunwaldlab.r-universe.dev
Date/Publication: 2025-06-13 18:38:48 UTC
RemoteUrl: https://github.com/grunwaldlab/demulticoder
RemoteRef: HEAD
RemoteSha: 1b828f933bee26b0c76497809f172af472e61939
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]