DESCRIPTION

Package: demulticoder
Title: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes
Version: 0.1.0
Authors@R: c(person("Martha A.", "Sudermann", email = "sudermam@oregonstate.edu", role = c("aut", "cre")), 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 = "aut")) 
Description: The demulticoder package provides a comprehensive workflow for analyzing multiplex metabarcode data. It includes robust wrappers for cutadapt and DADA2 to trim primers, filter reads, perform 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. 
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
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
URL: https://grunwaldlab.github.io/demulticoder/
BugReports: https://github.com/grunwaldlab/demulticoder/issues
RoxygenNote: 7.3.2
Config/Needs/website: rmarkdown
NeedsCompilation: no
Packaged: 2025-03-17 23:40:47 UTC; marthasudermann
Author: Martha A. Sudermann [aut, cre],
  Zachary S. L Foster [aut],
  Samantha Dawson [aut],
  Hung Phan [aut],
  Jeff H. Chang [aut],
  Niklaus Grünwald [aut]
Maintainer: Martha A. Sudermann <sudermam@oregonstate.edu>