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demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

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>.

Version: 0.1.2
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)
Published: 2025-05-05
DOI: 10.32614/CRAN.package.demulticoder
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]
Maintainer: Martha A. Sudermann <sudermam at oregonstate.edu>
BugReports: https://github.com/grunwaldlab/demulticoder/issues
License: MIT + file LICENSE
URL: https://grunwaldlab.github.io/demulticoder/, https://github.com/grunwaldlab/demulticoder
NeedsCompilation: no
Materials: README NEWS
CRAN checks: demulticoder results

Documentation:

Reference manual: demulticoder.pdf

Downloads:

Package source: demulticoder_0.1.2.tar.gz
Windows binaries: r-devel: demulticoder_0.1.2.zip, r-release: demulticoder_0.1.2.zip, r-oldrel: not available
macOS binaries: r-release (arm64): demulticoder_0.1.2.tgz, r-oldrel (arm64): demulticoder_0.1.2.tgz, r-release (x86_64): demulticoder_0.1.2.tgz, r-oldrel (x86_64): demulticoder_0.1.2.tgz

Linking:

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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.